Debian Med Project
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Summary
The Debian Med Pure Blend contains 1273 packages which are grouped by metapackages. Each metapackage will cause the installation of packages for a specific topic. The following table lists the metapackages of Debian Med

Tasks page

This is a list of the Tasks Debian Med is made of:

Table of contents

Biology - Debian Med bioinformatics packages

This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.

Official Debian packages with high relevance

Abacas
close gaps in genomic alignments from short reads
Abyss
de novo, parallel, sequence assembler for short reads
Acedb-other
retrieval of DNA or protein sequences
Adapterremoval
rapid adapter trimming, identification, and read merging of gene sequences
Adun-core
Molecular Simulator
Aegean
integrated genome analysis toolkit
Aevol
digital genetics model to run Evolution Experiments in silico
Alien-hunter
Interpolated Variable Order Motifs to identify horizontally acquired DNA
Alter-sequence-alignment
genomic sequences ALignment Transformation EnviRonment
Altree
program to perform phylogeny-based association and localization analysis
Amap-align
Protein multiple alignment by sequence annealing
Ampliconnoise
removal of noise from 454 sequenced PCR amplicons
Andi
Efficient Estimation of Evolutionary Distances
Anfo
Short Read Aligner/Mapper from MPG
Aragorn
tRNA and tmRNA detection in nucleotide sequences
Arden
specificity control for read alignments using an artificial reference
Ariba
Antibiotic Resistance Identification By Assembly
Art-nextgen-simulation-tools
simulation tools to generate synthetic next-generation sequencing reads
Artemis
genome browser and annotation tool
Artfastqgenerator
outputs artificial FASTQ files derived from a reference genome
Assembly-stats
get assembly statistics from FASTA and FASTQ files
Assemblytics
detect and analyze structural variants from a genome assembly
Atac
genome assembly-to-assembly comparison
Ataqv
ATAC-seq QC and visualization
Atropos
NGS read trimming tool that is specific, sensitive, and speedy
Augur
pipeline components for real-time virus analysis
Augustus
gene prediction in eukaryotic genomes
Autodock
analysis of ligand binding to protein structure
Autodock-vina
docking of small molecules to proteins
Autogrid
pre-calculate binding of ligands to their receptor
Avogadro
Molecular Graphics and Modelling System
Axe-demultiplexer
Trie-based DNA sequencing read demultiplexer
Baitfisher
software package for designing hybrid enrichment probes
Bali-phy
Bayesian Inference of Alignment and Phylogeny
Ballview
free molecular modeling and molecular graphics tool
Bamclipper
Remove gene-specific primer sequences from SAM/BAM alignments
Bamkit
tools for common BAM file manipulations
Bamtools
toolkit for manipulating BAM (genome alignment) files
Bandage
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Barrnap
rapid ribosomal RNA prediction
Bbmap
short read aligner and other bioinformatic tools
Bcalm
de Bruijn compaction in low memory
Bcftools
genomic variant calling and manipulation of VCF/BCF files
Beads
2-DE electrophoresis gel image spot detection
Beagle
Genotype calling, genotype phasing and imputation of ungenotyped markers
Beast-mcmc
Bayesian MCMC phylogenetic inference
Beast2-mcmc
Bayesian MCMC phylogenetic inference
Bedops
high-performance genomic feature operations
Bedtools
suite of utilities for comparing genomic features
Belvu
multiple sequence alignment viewer and phylogenetic tool
Berkeley-express
Streaming quantification for high-throughput sequencing
Bio-eagle
Haplotype phasing within a genotyped cohort or using a phased reference panel
Bio-rainbow
clustering and assembling short reads for bioinformatics
Bio-tradis
analyse the output from TraDIS analyses of genomic sequences
Bio-vcf
domain specific language (DSL) for processing the VCF format
Bioawk
extension of awk for biological sequence analysis
Biobambam2
tools for early stage alignment file processing
Biosyntax
Syntax Highlighting for Computational Biology (metapackage)
Bitseq
Bayesian Inference of Transcripts from Sequencing Data
Blasr
mapping single-molecule sequencing reads
Blixem
interactive browser of sequence alignments
Bolt-lmm
Efficient large cohorts genome-wide Bayesian mixed-model association testing
Bowtie
Ultrafast memory-efficient short read aligner
Bowtie2
ultrafast memory-efficient short read aligner
Boxshade
Pretty-printing of multiple sequence alignments
Bppphyview
Bio++ Phylogenetic Viewer
Bppsuite
Bio++ program suite
Brig
BLAST Ring Image Generator
Busco
benchmarking sets of universal single-copy orthologs
Bustools
program for manipulating BUS files for single cell RNA-Seq datasets
Bwa
Burrows-Wheeler Aligner
Canu
single molecule sequence assembler for genomes
Cassiopee
index and search tool in genomic sequences
Cat-bat
taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Cct
visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
Cd-hit
suite of programs designed to quickly group sequences
Cdbfasta
Constant DataBase indexing and retrieval tools for multi-FASTA files
Centrifuge
rapid and memory-efficient system for classification of DNA sequences
Cgview
Circular Genome Viewer
Changeo
Repertoire clonal assignment toolkit (Python 3)
Chimeraslayer
detects likely chimeras in PCR amplified DNA
Chromhmm
Chromatin state discovery and characterization
Chromimpute
Large-scale systematic epigenome imputation
Cif-tools
Suite of tools to manipulate, validate and query mmCIF files
Circlator
circularize genome assemblies
Circos
plotter for visualizing data
Clearcut
extremely efficient phylogenetic tree reconstruction
Clonalframe
inference of bacterial microevolution using multilocus sequence data
Clonalframeml
Efficient Inference of Recombination in Whole Bacterial Genomes
Clonalorigin
inference of homologous recombination in bacteria using whole genome sequences
Clustalo
General-purpose multiple sequence alignment program for proteins
Clustalw
global multiple nucleotide or peptide sequence alignment
Clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
Cnvkit
Copy number variant detection from targeted DNA sequencing
Codonw
Correspondence Analysis of Codon Usage
Concavity
predictor of protein ligand binding sites from structure and conservation
Conservation-code
protein sequence conservation scoring tool
Covtobed
convert the coverage track from a BAM file into a BED file
Crac
integrated RNA-Seq read analysis
Csb
Computational Structural Biology Toolbox (CSB)
Cutadapt
Clean biological sequences from high-throughput sequencing reads
Daligner
local alignment discovery between long nucleotide sequencing reads
Damapper
long read to reference genome mapping tool
Datamash
statistics tool for command-line interface
Dawg
simulate the evolution of recombinant DNA sequences
Dazzdb
manage nucleotide sequencing read data
Deepnano
alternative basecaller for MinION reads of genomic sequences
Delly
Structural variant discovery by read analysis
Density-fitness
Calculates per-residue electron density scores
Dextractor
(d)extractor and compression command library
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Diamond-aligner
accelerated BLAST compatible local sequence aligner
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder
cysteines disulfide bonding state and connectivity predictor
Dnaclust
tool for clustering millions of short DNA sequences
Dotter
detailed comparison of two genomic sequences
Drop-seq-tools
analyzing Drop-seq data
Dssp
protein secondary structure assignment based on 3D structure
Dwgsim
short sequencing read simulator
E-mem
Efficient computation of Maximal Exact Matches for very large genomes
Ea-utils
command-line tools for processing biological sequencing data
Ecopcr
estimate PCR barcode primers quality
Edtsurf
triangulated mesh surfaces for protein structures
Eigensoft
reduction of population bias for genetic analyses
Elph
DNA/protein sequence motif finder
Embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
Embassy-domalign
Extra EMBOSS commands for protein domain alignment
Embassy-domsearch
Extra EMBOSS commands to search for protein domains
Emboss
European molecular biology open software suite
Emmax
genetic mapping considering population structure
Estscan
ORF-independent detector of coding DNA sequences
Examl
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
Exonerate
generic tool for pairwise sequence comparison
Falcon
diploid-aware genome assembly of single-molecule sequencing reads
Fasta3
tools for searching collections of biological sequences
Fastahack
utility for indexing and sequence extraction from FASTA files
Fastaq
FASTA and FASTQ file manipulation tools
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Fastlink
faster version of pedigree programs of Linkage
Fastml
maximum likelihood ancestral amino-acid sequence reconstruction
Fastp
Ultra-fast all-in-one FASTQ preprocessor
Fastqc
quality control for high throughput sequence data
Fastqtl
Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
Fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
Ffindex
simple index/database for huge amounts of small files
Figtree
graphical phylogenetic tree viewer
Filtlong
quality filtering tool for long reads of genome sequences
Fitgcp
fitting genome coverage distributions with mixture models
Flash
Fast Length Adjustment of SHort reads
Flexbar
flexible barcode and adapter removal for sequencing platforms
Fml-asm
tool for assembling Illumina short reads in small regions
Freebayes
Bayesian haplotype-based polymorphism discovery and genotyping
Freecontact
fast protein contact predictor
Fsa
Fast Statistical Alignment of protein, RNA or DNA sequences
Fsm-lite
frequency-based string mining (lite)
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Garli
phylogenetic analysis of molecular sequence data using maximum-likelihood
Garlic
visualization program for biomolecules
Gasic
genome abundance similarity correction
Gatb-core
Genome Analysis Toolbox with de-Bruijn graph
Gbrowse
GMOD Generic Genome Browser
Gdpc
visualiser of molecular dynamic simulations
Gemma
Genome-wide Efficient Mixed Model Association
Genometester
toolkit for performing set operations on k-mer lists
Genomethreader
software tool to compute gene structure predictions
Genometools
versatile genome analysis toolkit
Gentle
suite to plan genetic cloning
Gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps
produces PostScript graphical output from GFF-files
Gffread
GFF/GTF format conversions, region filtering, FASTA sequence extraction
Ggd-utils
programs for use in ggd
Ghemical
GNOME molecular modelling environment
Ghmm
General Hidden-Markov-Model library - tools
Glam2
gapped protein motifs from unaligned sequences
Gmap
spliced and SNP-tolerant alignment for mRNA and short reads
Grabix
wee tool for random access into BGZF files
Graphlan
circular representations of taxonomic and phylogenetic trees
Grinder
Versatile omics shotgun and amplicon sequencing read simulator
Gromacs
Molecular dynamics simulator, with building and analysis tools
Gsort
sort genomic data
Gubbins
phylogenetic analysis of genome sequences
Gwama
Genome-Wide Association Meta Analysis
Harvest-tools
archiving and postprocessing for reference-compressed genomic multi-alignments
Hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
Hilive
realtime alignment of Illumina reads
Hinge
long read genome assembler based on hinging
Hisat2
graph-based alignment of short nucleotide reads to many genomes
Hmmer
profile hidden Markov models for protein sequence analysis
Hmmer2
profile hidden Markov models for protein sequence analysis
Hyphy-mpi
Hypothesis testing using Phylogenies (MPI version)
Hyphy-pt
Hypothesis testing using Phylogenies (pthreads version)
Idba
iterative De Bruijn Graph short read assemblers
Igdiscover
analyzes antibody repertoires to find new V genes
Igor
infers V(D)J recombination processes from sequencing data
Indelible
powerful and flexible simulator of biological evolution
Infernal
inference of RNA secondary structural alignments
Insilicoseq
sequencing simulator producing realistic Illumina reads
Ipig
integrating PSMs into genome browser visualisations
Iqtree
efficient phylogenetic software by maximum likelihood
Iva
iterative virus sequence assembler
Jaligner
Smith-Waterman algorithm with Gotoh's improvement
Jalview
multiple alignment editor
Jellyfish
count k-mers in DNA sequences
Jellyfish1
count k-mers in DNA sequences
Jmodeltest
HPC selection of models of nucleotide substitution
Jmol
Molecular Viewer
Kalign
Global and progressive multiple sequence alignment
Kallisto
near-optimal RNA-Seq quantification
Kaptive
obtain information about K and O types for Klebsiella genome assemblies
Khmer
in-memory DNA sequence kmer counting, filtering & graph traversal
Kineticstools
detection of DNA modifications
King-probe
Evaluate and visualize protein interatomic packing
Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
Kleborate
tool to screen Klebsiella genome assemblies
Kma
mapping genomic sequences to raw reads directly against redundant databases
Kmc
count kmers in genomic sequences
Kmer
suite of tools for DNA sequence analysis
Kmerresistance
correlates mapped genes with the predicted species of WGS samples
Kraken
assigning taxonomic labels to short DNA sequences
Kraken2
taxonomic classification system using exact k-mer matches
Lagan
highly parametrizable pairwise global genome sequence aligner
Lamarc
Likelihood Analysis with Metropolis Algorithm using Random Coalescence
Lambda-align
Local Aligner for Massive Biological DatA
Lambda-align2
Local Aligner for Massive Biological DatA - v2
Last-align
genome-scale comparison of biological sequences
Lastz
pairwise aligning DNA sequences
Leaff
biological sequence library utilities and applications
Lefse
determine features of organisms, clades, taxonomic units, genes
Librg-utils-perl
parsers and format conversion utilities used by (e.g.) profphd
Libvcflib-tools
C++ library for parsing and manipulating VCF files (tools)
Lighter
fast and memory-efficient sequencing error corrector
Logol
Pattern matching tool using Logol language
Loki
MCMC linkage analysis on general pedigrees
Ltrsift
postprocessing and classification of LTR retrotransposons
Lucy
DNA sequence quality and vector trimming tool
Lumpy-sv
general probabilistic framework for structural variant discovery
Macs
Model-based Analysis of ChIP-Seq on short reads sequencers
Macsyfinder
detection of macromolecular systems in protein datasets
Maffilter
process genome alignment in the Multiple Alignment Format
Mafft
Multiple alignment program for amino acid or nucleotide sequences
Mapdamage
tracking and quantifying damage patterns in ancient DNA sequences
Mapsembler2
bioinformatics targeted assembly software
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Maqview
graphical read alignment viewer for short gene sequences
Mash
fast genome and metagenome distance estimation using MinHash
Mauve-aligner
multiple genome alignment
Mecat2
ultra-fast and accurate de novo assembly tools for SMRT reads
Megahit
ultra-fast and memory-efficient meta-genome assembler
Melting
compute the melting temperature of nucleic acid duplex
Meryl
in- and out-of-core kmer counting and utilities
Metabat
robust statistical framework for reconstructing genomes from metagenomic data
Metaphlan2
Metagenomic Phylogenetic Analysis
Metastudent
predictor of Gene Ontology terms from protein sequence
Mhap
locality-sensitive hashing to detect long-read overlaps
Microbegps
explorative taxonomic profiling tool for metagenomic data
Microbiomeutil
Microbiome Analysis Utilities
Mindthegap
performs detection and assembly of DNA insertion variants in NGS read datasets
Minia
short-read biological sequence assembler
Miniasm
ultrafast de novo assembler for long noisy DNA sequencing reads
Minimac4
Fast Imputation Based on State Space Reduction HMM
Minimap
tool for approximate mapping of long biosequences such as DNA reads
Minimap2
versatile pairwise aligner for genomic and spliced nucleotide sequences
Mipe
Tools to store PCR-derived data
Mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
Mirtop
annotate miRNAs with a standard mirna/isomir naming
Mlv-smile
Find statistically significant patterns in sequences
Mmb
model the structure and dynamics of macromolecules
Mmseqs2
ultra fast and sensitive protein search and clustering
Mosdepth
BAM/CRAM depth calculation biological sequencing
Mothur
sequence analysis suite for research on microbiota
Mptp
single-locus species delimitation
Mrbayes
Bayesian Inference of Phylogeny
Msxpertsuite
mass spectrometry software suite - metapackage
Multiqc
output integration for RNA sequencing across tools and samples
Mummer
Efficient sequence alignment of full genomes
Murasaki
homology detection tool across multiple large genomes
Murasaki-mpi
homology detection tool across multiple large genomes (MPI-version)
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Nanofilt
filtering and trimming of long read sequencing data
Nanolyse
remove lambda phage reads from a fastq file
Nanook
pre- and post-alignment analysis of nanopore sequencing data
Nanopolish
consensus caller for nanopore sequencing data
Nanostat
statistics on long biological sequences
Nanosv
structural variant caller for nanopore data
Nast-ier
NAST-based DNA alignment tool
Ncbi-acc-download
download genome files from NCBI by accession
Ncbi-blast+
next generation suite of BLAST sequence search tools
Ncbi-blast+-legacy
NCBI Blast legacy call script
Ncbi-entrez-direct
NCBI Entrez utilities on the command line
Ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-seg
tool to mask segments of low compositional complexity in amino acid sequences
Ncbi-tools-bin
NCBI libraries for biology applications (text-based utilities)
Ncbi-tools-x11
NCBI libraries for biology applications (X-based utilities)
Ncl-tools
tools to deal with NEXUS files
Ncoils
coiled coil secondary structure prediction
Neobio
computes alignments of amino acid and nucleotide sequences
Ngmlr
CoNvex Gap-cost alignMents for Long Reads
Njplot
phylogenetic tree drawing program
Norsnet
tool to identify unstructured loops in proteins
Norsp
predictor of non-regular secondary structure
Obitools
programs to analyze NGS data in a DNA metabarcoding context
Openms
package for LC/MS data management and analysis
Optimir
Integrating genetic variations in miRNA alignment
Pal2nal
converts proteins to genomic DNA alignment
Paleomix
pipelines and tools for the processing of ancient and modern HTS data
Paml
Phylogenetic Analysis by Maximum Likelihood (PAML)
Paraclu
Parametric clustering of genomic and transcriptomic features
Parasail
Aligner based on libparasail3
Parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
Parsnp
rapid core genome multi-alignment
Patman
rapid alignment of short sequences to large databases
Pbdagcon
sequence consensus using directed acyclic graphs
Pbhoney
genomic structural variation discovery
Pbjelly
genome assembly upgrading tool
Pbsim
simulator for PacBio sequencing reads
Pbsuite
software for Pacific Biosciences sequencing data
Pdb2pqr
Preparation of protein structures for electrostatics calculations
Perlprimer
Graphical design of primers for PCR
Perm
efficient mapping of short reads with periodic spaced seeds
Pftools
build and search protein and DNA generalized profiles
Phast
phylogenetic analysis with space/time models
Phipack
PHI test and other tests of recombination
Phybin
binning/clustering newick trees by topology
Phylip
package of programs for inferring phylogenies
Phylonium
Fast and Accurate Estimation of Evolutionary Distances
Phyml
Phylogenetic estimation using Maximum Likelihood
Physamp
sample sequence alignment corresponding to phylogeny
Phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
Phyx
UNIX-style phylogenetic analyses on trees and sequences
Picard-tools
Command line tools to manipulate SAM and BAM files
Picopore
lossless compression of Nanopore files
Pigx-rnaseq
pipeline for checkpointed and distributed RNA-seq analyses
Piler
genomic repeat analysis
Pilercr
software for finding CRISPR repeats
Pilon
automated genome assembly improvement and variant detection tool
Pinfish
Collection of tools to annotate genomes using long read transcriptomics data
Pique
software pipeline for performing genome wide association studies
Pirs
Profile based Illumina pair-end Reads Simulator
Pizzly
Identifies gene fusions in RNA sequencing data
Placnet
Plasmid Constellation Network project
Plasmidid
mapping-based, assembly-assisted plasmid identification tool
Plasmidomics
draw plasmids and vector maps with PostScript graphics export
Plasmidseeker
identification of known plasmids from whole-genome sequencing reads
Plast
Parallel Local Sequence Alignment Search Tool
Plink
whole-genome association analysis toolset
Plink1.9
whole-genome association analysis toolset
Plink2
whole-genome association analysis toolset
Plip
fully automated protein-ligand interaction profiler
Poa
Partial Order Alignment for multiple sequence alignment
Populations
population genetic software
Porechop
adapter trimmer for Oxford Nanopore reads
Poretools
toolkit for nanopore nucleotide sequencing data
Pplacer
phylogenetic placement and downstream analysis
Prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Predictnls
prediction and analysis of protein nuclear localization signals
Presto
toolkit for processing B and T cell sequences
Prime-phylo
bayesian estimation of gene trees taking the species tree into account
Primer3
tool to design flanking oligo nucleotides for DNA amplification
Prinseq-lite
PReprocessing and INformation of SEQuence data (lite version)
Proalign
Probabilistic multiple alignment program
Probabel
Toolset for Genome-Wide Association Analysis
Probalign
multiple sequence alignment using partition function posterior probabilities
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prodigal
Microbial (bacterial and archaeal) gene finding program
Profbval
predictor of flexible/rigid protein residues from sequence
Profisis
prediction of protein-protein interaction sites from sequence
Profnet-bval
neural network architecture for profbval
Profnet-chop
neural network architecture for profchop
Profnet-con
neural network architecture for profcon
Profnet-isis
neural network architecture for profisis
Profnet-md
neural network architecture for metadisorder
Profnet-norsnet
neural network architecture for norsnet
Profnet-prof
neural network architecture for profacc
Profnet-snapfun
neural network architecture for snapfun
Profphd
secondary structure and solvent accessibility predictor
Profphd-net
neural network architecture for profphd
Profphd-utils
profphd helper utilities convert_seq and filter_hssp
Proftmb
per-residue prediction of bacterial transmembrane beta barrels
Progressivemauve
multiple genome alignment algorithms
Prokka
rapid annotation of prokaryotic genomes
Proteinortho
Detection of (Co-)orthologs in large-scale protein analysis
Prottest
selection of best-fit models of protein evolution
Pscan-chip
ChIP-based identifcation of TF binding sites
Pscan-tfbs
search for transcription factor binding sites
Psortb
bacterial localization prediction tool
Pycoqc
computes metrics and generates Interactive QC plots
Pycorrfit
tool for fitting correlation curves on a logarithmic plot
Pymol
Molecular Graphics System
Pyscanfcs
scientific tool for perpendicular line scanning FCS
Python3-biomaj3-daemon
BioMAJ daemon library
Python3-geneimpacts
wraps command line tools to assess variants in gene sequences
Python3-gffutils
Work with GFF and GTF files in a flexible database framework
Python3-pairtools
Framework to process sequencing data from a Hi-C experiment
Python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
Python3-sqt
SeQuencing Tools for biological DNA/RNA high-throughput data
Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Pyvcf
helper scripts for Variant Call Format (VCF) parser
Qcat
demultiplexing Oxford Nanopore reads from FASTQ files
Qcumber
quality control of genomic sequences
Qiime
Quantitative Insights Into Microbial Ecology
Qtltools
Tool set for molecular QTL discovery and analysis
Quicktree
Neighbor-Joining algorithm for phylogenies
Quorum
QUality Optimized Reads of genomic sequences
Qutemol
interactive visualization of macromolecules
R-bioc-annotate
BioConductor annotation for microarrays
R-bioc-biostrings
GNU R string objects representing biological sequences
R-bioc-bitseq
transcript expression inference and analysis for RNA-seq data
R-bioc-cner
CNE Detection and Visualization
R-bioc-cummerbund
tool for analysis of Cufflinks RNA-Seq output
R-bioc-deseq2
R package for RNA-Seq Differential Expression Analysis
R-bioc-ebseq
R package for RNA-Seq Differential Expression Analysis
R-bioc-edger
Empirical analysis of digital gene expression data in R
R-bioc-genefilter
methods for filtering genes from microarray experiments
R-bioc-geoquery
Get data from NCBI Gene Expression Omnibus (GEO)
R-bioc-hilbertvis
GNU R package to visualise long vector data
R-bioc-htsfilter
GNU R filter replicated high-throughput transcriptome sequencing data
R-bioc-impute
Imputation for microarray data
R-bioc-limma
linear models for microarray data
R-bioc-mergeomics
Integrative network analysis of omics data
R-bioc-metagenomeseq
GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-mofa
Multi-Omics Factor Analysis (MOFA)
R-bioc-multiassayexperiment
Software for integrating multi-omics experiments in BioConductor
R-bioc-mutationalpatterns
GNU R comprehensive genome-wide analysis of mutational processes
R-bioc-pcamethods
BioConductor collection of PCA methods
R-bioc-phyloseq
GNU R handling and analysis of high-throughput microbiome census data
R-bioc-rtracklayer
GNU R interface to genome browsers and their annotation tracks
R-bioc-scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
R-bioc-tfbstools
GNU R Transcription Factor Binding Site (TFBS) Analysis
R-cran-adegenet
GNU R exploratory analysis of genetic and genomic data
R-cran-adephylo
GNU R exploratory analyses for the phylogenetic comparative method
R-cran-alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-ape
GNU R package for Analyses of Phylogenetics and Evolution
R-cran-bio3d
GNU R package for biological structure analysis
R-cran-distory
GNU R distance between phylogenetic histories
R-cran-genabel
GNU R package for genome-wide SNP association analysis
R-cran-kaos
Encoding of Sequences Based on Frequency Matrix Chaos
R-cran-metamix
GNU R bayesian mixture analysis for metagenomic community profiling
R-cran-phangorn
GNU R package for phylogenetic analysis
R-cran-phytools
GNU R phylogenetic tools for comparative biology
R-cran-pscbs
R package: Analysis of Parent-Specific DNA Copy Numbers
R-cran-qtl
GNU R package for genetic marker linkage analysis
R-cran-rotl
GNU R interface to the 'Open Tree of Life' API
R-cran-samr
GNU R significance analysis of microarrays
R-cran-sdmtools
Species Distribution Modelling Tools
R-cran-seqinr
GNU R biological sequences retrieval and analysis
R-cran-seurat
Tools for Single Cell Genomics
R-cran-shazam
Immunoglobulin Somatic Hypermutation Analysis
R-cran-spp
GNU R ChIP-seq processing pipeline
R-cran-tcr
Advanced Data Analysis of Immune Receptor Repertoires
R-cran-tigger
Infers new Immunoglobulin alleles from Rep-Seq Data
R-cran-treescape
GNU R Statistical Exploration of Landscapes of Phylogenetic Trees
R-cran-tsne
t-distributed stochastic neighbor embedding for R (t-SNE)
R-cran-vegan
Community Ecology Package for R
R-cran-webgestaltr
find over-represented properties in gene lists
R-cran-wgcna
Weighted Correlation Network Analysis
R-other-ascat
Allele-Specific Copy Number Analysis of Tumours
R-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
R-other-rajewsky-dropbead
Basic Exploration and Analysis of Drop-seq Data
Racon
consensus module for raw de novo DNA assembly of long uncorrected reads
Radiant
explore hierarchical metagenomic data with zoomable pie charts
Ragout
Reference-Assisted Genome Ordering UTility
Rambo-k
Read Assignment Method Based On K-mers
Rampler
module for sampling genomic sequences
Rapmap
rapid sensitive and accurate DNA read mapping via quasi-mapping
Rasmol
visualization of biological macromolecules
Raster3d
tools for generating images of proteins or other molecules
Rate4site
detector of conserved amino-acid sites
Raxml
Randomized Axelerated Maximum Likelihood of phylogenetic trees
Ray
de novo genome assemblies of next-gen sequencing data
Rdp-alignment
Ribosomal Database Project (RDP) alignment tools package
Rdp-classifier
extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
Rdp-readseq
Ribosomal Database Project (RDP) sequence reading and writing
Readseq
Conversion between sequence formats
Readucks
Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
Reapr
universal tool for genome assembly evaluation
Recan
genetic distance plotting for recombination events analysis
Relion
toolkit for 3D reconstructions in cryo-electron microscopy
Relion-gui
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Repeatmasker-recon
finds repeat families from biological sequences
Reprof
protein secondary structure and accessibility predictor
Resfinder
identify acquired antimicrobial resistance genes
Rna-star
ultrafast universal RNA-seq aligner
Rnahybrid
Fast and effective prediction of microRNA/target duplexes
Roary
high speed stand alone pan genome pipeline
Roguenarok
versatile and scalable algorithm for rogue taxon identification
Rsem
RNA-Seq by Expectation-Maximization
Rtax
Classification of sequence reads of 16S ribosomal RNA gene
Runcircos-gui
GUI tool to run circos
Saint
Significance Analysis of INTeractome
Salmid
rapid Kmer based Salmonella identifier from sequence data
Salmon
wicked-fast transcript quantification from RNA-seq data
Sambamba
tools for working with SAM/BAM data
Samblaster
marks duplicates, extracts discordant/split reads
Samclip
filter SAM file for soft and hard clipped alignments
Samtools
processing sequence alignments in SAM, BAM and CRAM formats
Scoary
pangenome-wide association studies
Scrappie
basecaller for Nanopore sequencer
Scrm
simulator of evolution of genetic sequences
Scythe
Bayesian adaptor trimmer for sequencing reads
Seaview
Multiplatform interface for sequence alignment and phylogeny
Seer
genomic sequence element (kmer) enrichment analysis
Segemehl
short read mapping with gaps
Sepp
phylogeny with ensembles of Hidden Markov Models
Seqan-apps
C++ library for the analysis of biological sequences
Seqkit
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Seqmagick
imagemagick-like frontend to Biopython SeqIO
Seqprep
stripping adaptors and/or merging paired reads of DNA sequences with overlap
Seqsero
Salmonella serotyping from genome sequencing data
Seqtk
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sga
de novo genome assembler that uses string graphs
Shasta
nanopore whole genome assembly (binaries and scripts)
Shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
Sibelia
comparative genomics tool
Sibsim4
align expressed RNA sequences on a DNA template
Sickle
windowed adaptive trimming tool for FASTQ files using quality
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Sim4
tool for aligning cDNA and genomic DNA
Sim4db
batch spliced alignment of cDNA sequences to a target genome
Simka
comparative metagenomics method dedicated to NGS datasets
Simkamin
approximate comparative metagenomics method dedicated to NGS datasets
Skesa
strategic Kmer extension for scrupulous assemblies
Skewer
post-processing of high-throughput DNA sequence reads
Smalt
Sequence Mapping and Alignment Tool
Smithwaterman
determine similar regions between two strings or genomic sequences
Smrtanalysis
software suite for single molecule, real-time sequencing
Snap
location of genes from DNA sequence with hidden markov model
Snap-aligner
Scalable Nucleotide Alignment Program
Sniffles
structural variation caller using third-generation sequencing
Snp-sites
Binary code for the package snp-sites
Snpomatic
fast, stringent short-read mapping software
Soapaligner
aligner of short reads of next generation sequencers
Soapdenovo
short-read assembly method to build de novo draft assembly
Soapdenovo2
short-read assembly method to build de novo draft assembly
Soapsnp
resequencing utility that can assemble consensus sequence of genomes
Sortmerna
tool for filtering, mapping and OTU-picking NGS reads
Spaced
alignment-free sequence comparison using spaced words
Spades
genome assembler for single-cell and isolates data sets
Spaln
splicing-aware transcript-alignment to genomic DNA
Spoa
SIMD partial order alignment tool
Sprai
single-pass sequencing read accuracy improver
Spread-phy
analyze and visualize phylogeographic reconstructions
Squizz
Converter for genetic sequences and alignments
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Srst2
Short Read Sequence Typing for Bacterial Pathogens
Ssake
genomics application for assembling millions of very short DNA sequences
Sspace
scaffolding pre-assembled contigs after extension
Ssw-align
Smith-Waterman aligner based on libssw
Stacks
pipeline for building loci from short-read DNA sequences
Staden
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden-io-lib-utils
programs for manipulating DNA sequencing files
Stringtie
assemble short RNAseq reads to transcripts
Subread
toolkit for processing next-gen sequencing data
Suitename
categorize each suite in an RNA backbone
Sumaclust
fast and exact clustering of genomic sequences
Sumatra
fast and exact comparison and clustering of sequences
Sumtrees
Phylogenetic Tree Summarization and Annotation
Surankco
Supervised Ranking of Contigs in de novo Assemblies
Survivor
tool set for simulating/evaluating SVs
Svim
Structural variant caller for long sequencing reads
Swarm
robust and fast clustering method for amplicon-based studies
Sweed
assessment of SNPs for their evolutionary advantage
T-coffee
Multiple Sequence Alignment
Tabix
generic indexer for TAB-delimited genome position files
Tantan
low complexity and tandem repeat masker for biosequences
Theseus
superimpose macromolecules using maximum likelihood
Thesias
Testing Haplotype Effects In Association Studies
Tiddit
structural variant calling
Tigr-glimmer
Gene detection in archea and bacteria
Tm-align
structural alignment of proteins
Tnseq-transit
statistical calculations of essentiality of genes or genomic regions
Toil
cross-platform workflow engine
Tombo
identification of modified nucleotides from raw nanopore sequencing data
Tophat
fast splice junction mapper for RNA-Seq reads
Tophat-recondition
post-processor for TopHat unmapped reads
Topp
set of programs implementing The OpenMS Proteomic Pipeline
Toppred
transmembrane topology prediction
Tortoize
Application to calculate ramachandran z-scores
Trace2dbest
bulk submission of chromatogram data to dbEST
Tracetuner
interpretation of DNA Sanger sequencing data
Transdecoder
find coding regions within RNA transcript sequences
Transrate-tools
helper for transrate
Transtermhp
find rho-independent transcription terminators in bacterial genomes
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Treeview
Java re-implementation of Michael Eisen's TreeView
Treeviewx
Displays and prints phylogenetic trees
Trf
locate and display tandem repeats in DNA sequences
Trim-galore
automate quality and adapter trimming for DNA sequencing
Trimmomatic
flexible read trimming tool for Illumina NGS data
Trinityrnaseq
RNA-Seq De novo Assembly
Tvc
genetic variant caller for Ion Torrent sequencing platforms
Uc-echo
error correction algorithm designed for short-reads from NGS
Umap-learn
Uniform Manifold Approximation and Projection
Umis
tools for processing UMI RNA-tag data
Uncalled
Utility for Nanopore Current Alignment to Large Expanses of DNA
Unicycler
hybrid assembly pipeline for bacterial genomes
Varna
Visualization Applet for RNA
Vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads
Velvet-long
Nucleic acid sequence assembler for very short reads, long version
Velvetoptimiser
automatically optimise Velvet do novo assembly parameters
Vg
tools for working with genome variation graphs
Viewmol
graphical front end for computational chemistry programs
Virulencefinder
identify virulence genes in total or partial sequenced isolates of bacteria
Vmatch
large scale sequence analysis software
Vsearch
tool for processing metagenomic sequences
Vt
toolset for short variant discovery in genetic sequence data
Wham-align
Wisconsin's High-Throughput Alignment Method
Wigeon
reimplementation of the Pintail 16S DNA anomaly detection utility
Wise
comparison of biopolymers, like DNA and protein sequences
Yaha
find split-read mappings on single-end queries
Yanagiba
filter low quality Oxford Nanopore reads basecalled with Albacore
Yanosim
read simulator nanopore DRS datasets
Zalign
parallel local alignment of biological sequences

Official Debian packages with lower relevance

Adun.app
Molecular Simulator for GNUstep (GUI)
Conda-package-handling
create and extract conda packages of various formats
Dascrubber
alignment-based scrubbing pipeline for DNA sequencing reads
Dnapi
adapter prediction for small RNA sequencing - utils
Emboss-explorer
web-based GUI to EMBOSS
Epigrass
scientific tool for simulations and scenario analysis in network epidemiology
Getdata
management of external databases
Hts-nim-tools
tools biological sequences: bam-filter, count-reads, vcf-check
Idseq-bench
Benchmark generator for the IDseq Portal
Libhdf5-dev
HDF5 - development files - serial version
Libhnswlib-dev
fast approximate nearest neighbor search
Maude
high-performance logical framework
Metastudent-data
predictor of Gene Ontology terms from protein sequence - data files
Metastudent-data-2
predictor of Gene Ontology terms from protein sequence - data #2
Mrs
Information Retrieval System for Biomedical databanks
Python3-alignlib
edit and Hamming distances for biological sequences
Python3-anndata
annotated gene by sample numpy matrix
Python3-cgecore
Python3 module for the Center for Genomic Epidemiology
Python3-cyvcf2
VCF parser based on htslib (Python 3)
Python3-deeptools
platform for exploring biological deep-sequencing data
Python3-deeptoolsintervals
handlig GTF-like sequence-associated interal-annotation
Python3-htseq
Python3 high-throughput genome sequencing read analysis utilities
Python3-intake
lightweight package for finding and investigating data
Python3-loompy
access loom formatted files for bioinformatics
Python3-nanoget
extract information from Oxford Nanopore sequencing data and alignments
Python3-nanomath
simple math function for other Oxford Nanopore processing scripts
Python3-ncls
datastructure for interval overlap queries
Python3-py2bit
access to 2bit files
Python3-pybel
Biological Expression Language
Python3-pychopper
identify, orient and trim full-length Nanopore cDNA reads
Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
Python3-pyflow
lightweight parallel task engine for Python
Python3-pyranges
2D representation of genomic intervals and their annotations
Python3-pyrle
run length arithmetic in Python
Python3-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-tinyalign
numerical representation of differences between strings
Q2-alignment
QIIME 2 plugin for generating and manipulating alignments
Q2-cutadapt
QIIME 2 plugin to work with adapters in sequence data
Q2-dada2
QIIME 2 plugin to work with adapters in sequence data
Q2-demux
QIIME 2 plugin for demultiplexing of sequence reads
Q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
Q2-feature-table
QIIME 2 plugin supporting operations on feature tables
Q2-metadata
QIIME 2 plugin for working with and visualizing Metadata
Q2-quality-control
QIIME 2 plugin for quality assurance of feature and sequence data
Q2-quality-filter
QIIME2 plugin for PHRED-based filtering and trimming
Q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data
Q2-taxa
QIIME 2 plugin for working with feature taxonomy annotations
Q2-types
QIIME 2 plugin defining types for microbiome analysis
Q2cli
Click-based command line interface for QIIME 2
Q2templates
Design template package for QIIME 2 Plugins
R-bioc-annotationhub
GNU R client to access AnnotationHub resources
R-bioc-aroma.light
BioConductor methods normalization and visualization of microarray data
R-bioc-beachmat
I/O for several formats storing matrix data
R-bioc-biocneighbors
Nearest Neighbor Detection for Bioconductor Packages
R-bioc-biocsingular
Singular Value Decomposition for Bioconductor Packages
R-bioc-ctc
Cluster and Tree Conversion
R-bioc-dnacopy
R package: DNA copy number data analysis
R-bioc-ensembldb
GNU R utilities to create and use an Ensembl based annotation database
R-bioc-experimenthub
BioConductor client to access ExperimentHub resources
R-bioc-geneplotter
R package of functions for plotting genomic data
R-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
R-bioc-genomicfiles
Distributed computing by file or by range
R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
R-bioc-go.db
annotation maps describing the entire Gene Ontology
R-bioc-grohmm
GRO-seq Analysis Pipeline
R-bioc-gviz
Plotting data and annotation information along genomic coordinates
R-bioc-org.hs.eg.db
genome-wide annotation for Human
R-bioc-qusage
qusage: Quantitative Set Analysis for Gene Expression
R-bioc-savr
GNU R parse and analyze Illumina SAV files
R-bioc-singlecellexperiment
S4 Classes for Single Cell Data
R-bioc-structuralvariantannotation
Variant annotations for structural variants
R-bioc-tximport
transcript-level estimates for biological sequencing
R-cran-amap
Another Multidimensional Analysis Package
R-cran-biwt
biweight mean vector and covariance and correlation
R-cran-boolnet
assembling, analyzing and visualizing Boolean networks
R-cran-corrplot
Visualization of a Correlation Matrix
R-cran-dynamictreecut
Methods for Detection of Clusters in Hierarchical Clustering
R-cran-epir
GNU R Functions for analysing epidemiological data
R-cran-fitdistrplus
support fit of parametric distribution
R-cran-forecast
GNU R forecasting functions for time series and linear models
R-cran-gprofiler
Interface to the 'g:Profiler' Toolkit
R-cran-minerva
Maximal Information-Based Nonparametric Exploration
R-cran-optimalcutpoints
Computing Optimal Cutpoints in Diagnostic Tests
R-cran-parmigene
Parallel Mutual Information to establish Gene Networks
R-cran-pheatmap
GNU R package to create pretty heatmaps
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
R-cran-rcpphnsw
R bindings for a Library for Approximate Nearest Neighbors
R-cran-rentrez
GNU R interface to the NCBI's EUtils API
R-cran-rsgcc
Gini correlation and clustering of gene expression data
R-cran-sctransform
Variance Stabilizing Transformations for Single Cell UMI Data
Resfinder-db
ResFinder database is a curated database of acquired resistance genes
Science-workflow
workflow management systems useful for scientific research

Debian packages in contrib or non-free

Arb
phylogenetic sequence analysis suite - main program
Bcbio
toolkit for analysing high-throughput sequencing data
Blimps-utils
blocks database improved searcher
Caftools
maintenance of DNA sequence assemblies
Cluster3
Reimplementation of the Eisen-clustering software
Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip
EMBOSS conversions of the programs in the phylip package
Igv
Integrative Genomics Viewer
Raccoon
preparation of in silico drug screening projects
Relion-cuda
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Relion-gui-cuda
parallel toolkit for 3D reconstructions in cryo-electron microscopy
Seq-gen
simulate the evolution of nucleotide or amino acid sequences
Seqcluster
analysis of small RNA in NGS data
Sift
predicts if a substitution in a protein has a phenotypic effect
Solvate
arranges water molecules around protein structures
Trnascan-se
detection of transfer RNA genes in genomic sequence
Ugene
integrated bioinformatics toolkit
Varscan
variant detection in next-generation sequencing data
Vdjtools
framework for post-analysis of B/T cell repertoires
Vienna-rna
RNA sequence analysis

Debian packages in New queue (hopefully available soon)

Fastani
Fast alignment-free computation of whole-genome Average Nucleotide Identity
Snpeff
genetic variant annotation and effect prediction toolbox - tool

Packaging has started and developers might try the packaging code in VCS

Acacia
Error-corrector for pyrosequenced amplicon reads.
Agat
another GFF analysis toolkit
Amos-assembler
modular whole genome assembler
Apollo
genome annotation viewer and editor
Arvados
managing and analyzing biomedical big data
Axparafit
optimized statistical analysis of host-parasite coevolution
Axpcoords
highly optimized and parallelized porting of pcoords
Bagpipe
genomewide LD mapping
Bax2bam
Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format
Biceps
error-tolerant peptide identification
Bigsdb
Bacterial Isolate Genome Sequence Database
Bismark
bisulfite read mapper and methylation caller
Blat
BLAST-like alignment tool
Blobology
tool set for the visualisation of genome assemblies
Braker
annotating protein coding genes in genomes.
Card-rgi
analysis of genome sequences using the Resistance Gene Identifier
Cellprofiler
quantitatively measure phenotypes from images automatically
Cinema
multi-sequence alignment editor and viewer
Condetri
straight-forward trimming of FASTQ sequences
Contrafold
CONditional TRAining for RNA Secondary Structure Prediction
Coot
model building program for macromolecular crystallography
Covpipe
pipeline to generate consensus sequences from NGS reads
Crossbow
Genotyping from short reads using cloud computing
Crux-toolkit
toolkit for tandem mass spectrometry analysis
Cytoscape
visualizing molecular interaction networks
Dazzle
Java-based DAS server
Deepbinner
demultiplexing barcoded Oxford Nanopore sequencing reads
Dendroscope
analyzing and visualizing rooted phylogenetic trees and networks
Ecell
Concept and environment for constructing virtual cells on computers
Ensembl
basic Ensembl genome browser
Ensembl-vep
Variant Effect Predictor predicting the functional effects of genomic variants
Euler-sr
correcting errors in short gene sequence reads and assembling them
Euler2
de novo repeat classification and fragment assembly
Exabayes
bayesian phylogenetic tree inference for large-scale analyses
Ffp
Feature Frequency Profile Phylogeny
Fieldbioinformatics
pipeline with virus identification with Nanopore sequencer
Flappie
flip-flop basecaller for Oxford Nanopore reads
Flye
de novo assembler for single molecule sequencing reads using repeat graphs
Forester
Graphical vizualiation tool Archaeopteryx
Galaxy
scientific workflow and data integration platform for computational biology
Gatk
The Genome Analysis Toolkit
Gerp++
identifies constrained elements in multiple alignments
Gramalign
multiple alignment of biological sequences
Graphbin
refined binning of metagenomic contigs using assembly graphs
Graphmap2
highly sensitive and accurate mapper for long, error-prone reads
Hawkeye
Interactive Visual Analytics Tool for Genome Assemblies
Htqc
Quality control and filtration for illumina sequencing data
Idefix
index checking for improved demultiplexing of NGS data
Inspect
mass-spectrometry database search tool
Jbrowse
genome browser with an AJAX-based interface
Kempbasu
significance tests for comparing digital gene expression profiles
Lofreq
sensitive variant calling from sequencing data
Mach-haplotyper
Markov Chain based SNP haplotyper
Mage2tab
MAGE-MLv1 converter and visualiser
Malt
MEGAN alignment tool
Manta
structural variant and indel caller for mapped sequencing data
Marginphase
simultaneous haplotyping and genotyping
Martj
distributed data integration system for biological data
Mcaller
find methylation in nanopore reads
Medaka
sequence correction provided by ONT Research
Meme
search for common motifs in DNA or protein sequences
Mesquite
modular system for evolutionary analysis
Metabit
analysing microbial profiles from high-throughput sequencing shotgun data
Modeller
Protein structure modeling by satisfaction of spatial restraints
Molekel
Advanced Interactive 3D-Graphics for Molecular Sciences
Mosaik-aligner
reference-guided aligner for next-generation sequencing
Mpsqed
alignment editor and multiplex pyrosequencing assay designer
Mugsy
multiple whole genome alignment tool
Mview
biological sequence alignment conversion
Nanocall
Basecaller for Oxford Nanopore Sequencing Data
Nanocomp
compare multiple runs of long biological sequences
Nanoplot
plotting scripts for long read sequencing data
Ncbi-magicblast
RNA-seq mapping tool
Nextsv
automated structural variation detection for long-read sequencing
Ngila
global pairwise alignments with logarithmic and affine gap costs
Ngsqctoolkit
toolkit for the quality control of next generation sequencing data
Nw-align
global protein sequence alignment
Oases
de novo transcriptome assembler for very short reads
Omegamap
describing selection and recombination in sequences
Oncofuse
predicting oncogenic potential of gene fusions
Optitype
precision HLA typing from next-generation sequencing data
Paipline
Pipeline for the Automatic Identification of Pathogens
Pangolin
Phylogenetic Assignment of Named Global Outbreak LINeages
Partitionfinder
choses partitioning schemes and models of molecular evolution for sequence data
Patristic
Calculate patristic distances and comparing the components of genetic change
Pcma
fast and accurate multiple sequence alignment based on profile consistency
Phylophlan
microbial Tree of Life using 400 universal proteins
Phyloviz-core
phylogenetic inference and data visualization for sequence based typing methods
Pigx-scrnaseq
pipeline for checkpointed and distributed scRNA-seq analyses
Pipasic
Protein Abundance Correction in Metaproteomic Data
Plato
Analysis, translation, and organization of large-scale genetic data
Pomoxis
analysis components from Oxford Nanopore Research
Profit
Protein structure alignment
Psipred
protein secondary structure prediction
Pssh2
set of scripts for mapping protein sequence to structure
Pufferfish
An efficient index for the colored, compacted, de Bruijn graph
Purple
Picking Unique Relevant Peptides for viraL Experiments
Python3-emperor
visualizing high-throughput microbial community data
Q2-fragment-insertion
QIIME 2 plugin for fragment insertion
Q2-vsearch
QIIME 2 plugin for clustering and dereplicating with vsearch
Qtlreaper
QTL analysis for expression data
Qualimap
evaluating next generation sequencing alignment data
Quast
Quality Assessment Tool for Genome Assemblies
R-bioc-org.mm.eg.db
genome wide annotation for Mouse
R-cran-drinsight
drug repurposing on transcriptome sequencing data
R-other-apmswapp
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
R-other-fastbaps
A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
Raxml-ng
phylogenetic tree inference tool which uses maximum-likelihood
Repeatmasker
screen DNA sequences for interspersed repeats
Roadtrips
case-control association testing with unknown population and pedigree structure
Rosa
Removal of Spurious Antisense in biological RNA sequences
Rsat
Regulatory Sequence Analysis Tools
Sailfish
RNA-seq expression estimation
Sap
Pairwise protein structure alignment via double dynamic programming
Seq-seq-pan
workflow for the SEQuential alignment of SEQuences
Sequenceconverter.app
biological sequence file format conversion applet for GNUstep
Seqwish
alignment to variation graph inducer
Signalalign
HMM-HDP models for MinION signal alignments
Sina
reference based multiple sequence alignment
Sistr
Salmonella In Silico Typing Resource (SISTR)
Situs
Modeling of atomic resolution structures into low-resolution density maps
Sourmash
tools for comparing DNA sequences with MinHash sketches
Sparta
automated reference-based bacterial RNA-seq Transcriptome Analysis
Ssaha
Sequence Search and Alignment by Hashing Algorithm
Strap
Comfortable and intuitive protein alignment editor / viewer
Strap-base
essential files for the interactive alignment viewer and editor Strap
Strelka
strelka2 germline and somatic small variant caller
Tab2mage
submitting large microarray experiment datasets to public repository database
Tacg
command line program for finding patterns in nucleic acids
Tide
SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
Tigr-glimmer-mg
finding genes in environmental shotgun DNA sequences
Tn-seqexplorer
explore and analyze Tn-seq data for prokaryotic genomes
Ufasta
utility to manipulate fasta files
Umap
quantify genome and methylome mappability
Unc-fish
Fast Identification of Segmental Homology
Varmatch
robust matching of small genomic variant datasets
Vmd
presentation of traces of molecular dynamics runs
Zodiac-zeden
ZODIAC - Zeden's Organise DIsplay And Compute

Unofficial packages built by somebody else

Big-blast
Helper tool to run blast on large sequences
Estferret
processes, clusters and annotates EST data
Maxd
data warehouse and visualisation environment for genomic expression data
Migrate
estimation of population sizes and gene flow using the coalescent
Msatfinder
identification and characterization of microsatellites in a comparative genomic context
Oligoarrayaux
Prediction of Melting Profiles for Nucleic Acids
Partigene
generating partial gemomes
Pfaat
Protein Family Alignment Annotation Tool
Prot4est
EST protein translation suite
Python3-orange
Data mining framework
Qtlcart
map quantitative traits using a map of molecular markers
Rbs-finder
find ribosome binding sites(RBS)
Roche454ace2caf
convert GS20 or FLX assemblies into CAF format
Splitstree
Analyzing and Visualizing Evolutionary Data
Taverna
designing and executing myGrid workflows for bioinformatics
Taxinspector
browser for entries in the NCBI taxonomy
Tetra
tetranucleotide frequency calculator

No known packages available but some record of interest (WNPP bug)

Btk-core
biomolecule Toolkit C++ library
Mirbase
The microRNA sequence database
Phylowin
Graphical interface for molecular phylogenetic inference

No known packages available

Amoscmp
comparative genome assembly package
Annovar
annotate genetic variants detected from diverse genomes
Arachne
toolkit for Whole Genome Shotgun Assembly
Asap
organize the data associated with a genome
Bambus
hierarchical approach to building contig scaffolds
Cactus
Cdna-db
quality-control checking of finished cDNA clone sequences
Cmap
view comparisons of genetic and physical maps
Contralign
parameter learning framework for protein pairwise sequence alignment
Copycat
fast access to cophylogenetic analyses
E-hive
distributed processing system based on 'autonomous agents'
Exalt
phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
Excavator
gene expression data clustering
Figaro
novel vector trimming software
Forge
genome assembler for mixed read types
Gbrowse-syn
Generic Synteny Browser
Genemark
family of gene prediction programs
Genesplicer
computational method for splice site prediction
Genetrack
genomic data storage and visualization framework
Genezilla
eukaryotic gene finder
Genographer
read data and reconstruct them into a gel image
Glimmerhmm
Eukaryotic Gene-Finding System
Gmv
comparative genome browser for Murasaki
Jigsaw
gene prediction using multiple sources of evidence
Maker2
annotate genomes and create genome databases
Metarep
JCVI Metagenomics Reports
Minimus
AMOS lightweight assembler
Mummergpu
High-throughput sequence alignment using Graphics Processing Units
Obo-edit
editor for biological ontologies
Operondb
detect and analyze conserved gene pairs
Phagefinder
heuristic computer program to identify prophage regions within bacterial genomes
Phpphylotree
draw phylogenetic trees
Phylographer
Graph Visualization Tool
Pyrophosphate-tools
for assembling and searching pyrophosphate sequence data
Rose
Region-Of-Synteny Extractor
Treebuilder3d
viewer of SAGE and other types of gene expression data
Tripal
collection of Drupal modules for genomic research
Twain
syntenic genefinder employing a Generalized Pair Hidden Markov Model
Uniprime
workflow-based platform for universal primer design
X-tandem-pipeline
peptide/protein identification from MS/MS mass spectra

Biology development - Debian Med packages for development of bioinformatics applications

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Official Debian packages with high relevance

Bio-tradis
analyse the output from TraDIS analyses of genomic sequences
Biobambam2
tools for early stage alignment file processing
Bioperl
Perl tools for computational molecular biology
Bioperl-run
BioPerl wrappers: scripts
Biosquid
utilities for biological sequence analysis
Cwltool
Common Workflow Language reference implementation
Gffread
GFF/GTF format conversions, region filtering, FASTA sequence extraction
Libace-perl
Object-Oriented Access to ACEDB Databases
Libai-fann-perl
Perl wrapper for the FANN library
Libbambamc-dev
Development files for reading and writing BAM (genome alignment) files
Libbamtools-dev
C++ API for manipulating BAM (genome alignment) files
Libbigwig-dev
C library for handling bigWig files - header files
Libbio-alignio-stockholm-perl
stockholm sequence input/output stream
Libbio-asn1-entrezgene-perl
parser for NCBI Entrez Gene and NCBI Sequence records
Libbio-chado-schema-perl
DBIx::Class layer for the Chado database schema
Libbio-cluster-perl
BioPerl cluster modules
Libbio-coordinate-perl
BioPerl modules for working with biological coordinates
Libbio-das-lite-perl
implementation of the BioDas protocol
Libbio-db-biofetch-perl
Database object interface to BioFetch retrieval
Libbio-db-embl-perl
Database object interface for EMBL entry retrieval
Libbio-db-hts-perl
Perl interface to the HTS library
Libbio-db-ncbihelper-perl
collection of routines useful for queries to NCBI databases
Libbio-eutilities-perl
BioPerl interface to the Entrez Programming Utilities (E-utilities)
Libbio-featureio-perl
Modules for reading, writing, and manipulating sequence features
Libbio-graphics-perl
Generate GD images of Bio::Seq objects
Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
Libbio-mage-utils-perl
Extra modules for classes in the MAGE package: MAGE
Libbio-primerdesigner-perl
Perl module to design PCR primers using primer3 and epcr
Libbio-samtools-perl
Perl interface to SamTools library for DNA sequencing
Libbio-scf-perl
Perl extension for reading and writing SCF sequence files
Libbio-tools-phylo-paml-perl
Bioperl interface to the PAML suite
Libbio-tools-run-alignment-clustalw-perl
Bioperl interface to Clustal W
Libbio-tools-run-alignment-tcoffee-perl
Bioperl interface to T-Coffee
Libbio-tools-run-remoteblast-perl
Object for remote execution of the NCBI Blast via HTTP
Libbio-variation-perl
BioPerl variation-related functionality
Libbiococoa-dev
Bioinformatics framework for GNUstep and Cocoa (development files)
Libbiod-dev
bioinformatics library in D (development files)
Libbiojava-java
Java API to biological data and applications (default version)
Libbiojava4-java
Java API to biological data and applications (default version)
Libbioparser-dev
library for parsing several formats in bioinformatics
Libblasr-dev
tools for aligning PacBio reads to target sequences (development files)
Libbpp-core-dev
Bio++ Core library development files
Libbpp-phyl-dev
Bio++ Phylogenetic library development files
Libbpp-phyl-omics-dev
Bio++ Phylogenetics library: genomics components (development files)
Libbpp-popgen-dev
Bio++ Population Genetics library development files
Libbpp-qt-dev
Bio++ Qt Graphic classes library development files
Libbpp-raa-dev
Bio++ Remote Acnuc Access library development files
Libbpp-seq-dev
Bio++ Sequence library development files
Libbpp-seq-omics-dev
Bio++ Sequence library: genomics components (development files)
Libcdk-java
Chemistry Development Kit (CDK) Java libraries
Libchado-perl
database schema and tools for genomic data
Libcifpp-dev
Development files for libcifpp
Libconsensuscore-dev
algorithms for PacBio multiple sequence consensus -- development files
Libdivsufsort-dev
libdivsufsort header files
Libedlib-dev
library for sequence alignment using edit distance (devel)
Libfast5-dev
library for reading Oxford Nanopore Fast5 files -- headers
Libfastahack-dev
library for indexing and sequence extraction from FASTA files (devel)
Libffindex0-dev
library for simple index/database for huge amounts of small files (development)
Libfml-dev
development headers for libfml
Libgatbcore-dev
development library of the Genome Analysis Toolbox
Libgclib-dev
header files for Genome Code Lib (GCLib)
Libgenome-dev
toolkit for developing bioinformatic related software (devel)
Libgenome-model-tools-music-perl
module for finding mutations of significance in cancer
Libgenome-perl
pipelines, tools, and data management for genomics
Libgenometools0-dev
development files for GenomeTools
Libgff-dev
GFF/GTF parsing from cufflinks as a library
Libgkarrays-dev
library to query large collection of NGS sequences (development)
Libgo-perl
perl modules for GO and other OBO ontologies
Libhdf5-dev
HDF5 - development files - serial version
Libhmsbeagle-dev
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
Libhts-dev
development files for the HTSlib
Libhtscodecs-dev
Development headers for custom compression for CRAM and others
Libhtsjdk-java
Java API for high-throughput sequencing data (HTS) formats
Libjebl2-java
Java Evolutionary Biology Library
Libjloda-java
Java library of data structures and algorithms for bioinformatics
Libkmer-dev
suite of tools for DNA sequence analysis (development lib)
Libmems-dev
development library to support DNA string matching and comparative genomics
Libminimap2-dev
development headers for libminimap
Libmmblib-dev
development files of MacroMoleculeBuilder
Libmuscle-dev
multiple alignment development library for protein sequences
Libncbi-vdb-dev
libraries for using data in the INSDC Sequence Read Archives (devel)
Libncbi6-dev
NCBI libraries for biology applications (development files)
Libncl-dev
NEXUS Class Library (static lib and header files)
Libngs-java
Next Generation Sequencing language Bindings (Java bindings)
Libngs-sdk-dev
Next Generation Sequencing language Bindings (development)
Libnhgri-blastall-perl
Perl extension for running and parsing NCBI's BLAST 2.x
Libopenmm-dev
C++ header files for the OpenMM library
Libopenms-dev
library for LC/MS data management and analysis - dev files
Libpal-java
Phylogenetic Analysis Library
Libparasail-dev
Development heaaders and static libraries for parasail
Libpbbam-dev
Pacific Biosciences binary alignment/map (BAM) library (headers)
Libpbdata-dev
tools for handling PacBio sequences (development files)
Libpbihdf-dev
tools for handling PacBio hdf5 files (development files)
Libpbseq-dev
library for analyzing PacBio sequencing data (development files)
Libpdb-redo-dev
Development files for libpdb-redo
Libpll-dev
Phylogenetic Likelihood Library (development)
Libqes-dev
DNA sequence parsing library -- development
Librcsb-core-wrapper0-dev
development files for librcsb-core-wrapper0
Librdp-taxonomy-tree-java
taxonomy tree library from Ribosomal Database Project (RDP)
Librelion-dev
C++ API for RELION (3D reconstructions in cryo-electron microscopy)
Librg-blast-parser-perl
very fast NCBI BLAST parser - binding for Perl
Librg-reprof-bundle-perl
protein secondary structure and accessibility predictor (perl module)
Librostlab-blast0-dev
very fast C++ library for parsing the output of NCBI BLAST programs (devel)
Librostlab3-dev
C++ library for computational biology (development)
Libsbml5-dev
System Biology Markup Language library - development files
Libseqan2-dev
C++ library for the analysis of biological sequences (development)
Libseqan3-dev
C++ library for the analysis of biological sequences v3 (development)
Libseqlib-dev
C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
Libsmithwaterman-dev
determine similar regions between two strings or genomic sequences (devel)
Libsnp-sites1-dev
Static libraries and header files for the package snp-sites
Libsort-key-top-perl
Perl module to select and sort top n elements of a list
Libspoa-dev
SIMD partial order alignment library (development files)
Libsrf-dev
C++ implementation of the SRF format for DNA sequence data
Libssm-dev
macromolecular superposition library - development files
Libssw-dev
Development headers and static libraries for libssw
Libssw-java
Java bindings for libssw
Libstaden-read-dev
development files for libstaden-read
Libstatgen-dev
development files for the libStatGen
Libswiss-perl
Perl API to the UniProt database
Libtabixpp-dev
C++ wrapper to tabix indexer (development files)
Libthread-pool-dev
C++ header-only thread pool library (devel)
Libvcflib-dev
C++ library for parsing and manipulating VCF files (development)
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
Libzerg-perl
fast perl module for parsing the output of NCBI BLAST programs
Libzerg0-dev
development libraries and header files for libzerg
Mcl
Markov Cluster algorithm
Nim-hts-dev
wrapper for hts C library
Nim-kexpr-dev
kexpr math expressions for nim
Nim-lapper-dev
simple, fast interval searches for nim
Pyfai
Fast Azimuthal Integration scripts
Python3-airr
Data Representation Standard library for antibody and TCR sequences
Python3-anndata
annotated gene by sample numpy matrix
Python3-bcbio-gff
Python3 library to read and write Generic Feature Format
Python3-biom-format
Biological Observation Matrix (BIOM) format (Python 3)
Python3-biomaj3
BioMAJ workflow management library
Python3-biopython
Python3 library for bioinformatics
Python3-biotools
Python3 bioinformatics utilities for high-throughput genomic sequencing
Python3-bx
library to manage genomic data and its alignment
Python3-cgecore
Python3 module for the Center for Genomic Epidemiology
Python3-cobra
constraint-based modeling of biological networks with Python 3
Python3-cooler
library for a sparse, compressed, binary persistent storage
Python3-corepywrap
library that exports C++ mmCIF accessors to Python3
Python3-csb
Python framework for structural bioinformatics (Python3 version)
Python3-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 3)
Python3-cyvcf2
VCF parser based on htslib (Python 3)
Python3-deeptools
platform for exploring biological deep-sequencing data
Python3-deeptoolsintervals
handlig GTF-like sequence-associated interal-annotation
Python3-dendropy
DendroPy Phylogenetic Computing Library (Python 3)
Python3-dnaio
Python 3 library for fast parsing of FASTQ and FASTA files
Python3-ete3
Python Environment for (phylogenetic) Tree Exploration - Python 3.X
Python3-fast5
library for reading Oxford Nanopore Fast5 files -- Python 3
Python3-freecontact
fast protein contact predictor - binding for Python3
Python3-gfapy
flexible and extensible software library for handling sequence graphs
Python3-gffutils
Work with GFF and GTF files in a flexible database framework
Python3-htseq
Python3 high-throughput genome sequencing read analysis utilities
Python3-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 3 library
Python3-kineticstools
detection of DNA modifications (Python 3 library)
Python3-loompy
access loom formatted files for bioinformatics
Python3-mirtop
annotate miRNAs with a standard mirna/isomir naming (Python 3)
Python3-nanoget
extract information from Oxford Nanopore sequencing data and alignments
Python3-ngs
Next Generation Sequencing language Bindings (Python3 bindings)
Python3-pairix
1D/2D indexing and querying with a pair of genomic coordinates
Python3-parasail
Python3 bindings for the parasail C library
Python3-pbcommand
common command-line interface for Pacific Biosciences analysis modules
Python3-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 3
Python3-pbcore
Python 3 library for processing PacBio data files
Python3-peptidebuilder
generate atomic oligopeptide 3D structure from sequence
Python3-presto
toolkit for processing B and T cell sequences (Python3 module)
Python3-py2bit
access to 2bit files
Python3-pyani
Python3 module for average nucleotide identity analyses
Python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
Python3-pybel
Biological Expression Language
Python3-pybigwig
Python 3 module for quick access to bigBed and bigWig files
Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
Python3-pymummer
Python 3 interface to MUMmer
Python3-pyranges
2D representation of genomic intervals and their annotations
Python3-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-pyvcf
Variant Call Format (VCF) parser for Python 3
Python3-rdkit
Collection of cheminformatics and machine-learning software
Python3-ruffus
Python3 computation pipeline library widely used in bioinformatics
Python3-screed
short nucleotide read sequence utils in Python 3
Python3-shasta
nanopore whole genome assembly (dynamic library)
Python3-skbio
Python3 data structures, algorithms, educational resources for bioinformatic
Python3-sqt
SeQuencing Tools for biological DNA/RNA high-throughput data
Python3-streamz
build pipelines to manage continuous streams of data
Python3-tinyalign
numerical representation of differences between strings
Python3-torch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Python3-wdlparse
Workflow Description Language (WDL) parser for Python
R-bioc-biobase
base functions for Bioconductor
R-cran-boolnet
assembling, analyzing and visualizing Boolean networks
R-cran-corrplot
Visualization of a Correlation Matrix
R-cran-distory
GNU R distance between phylogenetic histories
R-cran-fitdistrplus
support fit of parametric distribution
R-cran-forecast
GNU R forecasting functions for time series and linear models
R-cran-genetics
GNU R package for population genetics
R-cran-gprofiler
Interface to the 'g:Profiler' Toolkit
R-cran-haplo.stats
GNU R package for haplotype analysis
R-cran-metamix
GNU R bayesian mixture analysis for metagenomic community profiling
R-cran-phangorn
GNU R package for phylogenetic analysis
R-cran-pheatmap
GNU R package to create pretty heatmaps
R-cran-phylobase
GNU R base package for phylogenetic structures and comparative data
R-cran-pscbs
R package: Analysis of Parent-Specific DNA Copy Numbers
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
R-cran-rentrez
GNU R interface to the NCBI's EUtils API
R-cran-rncl
GNU R interface to the Nexus Class Library
R-cran-rnexml
GNU R package for semantically rich I/O for the 'NeXML' format
R-cran-rotl
GNU R interface to the 'Open Tree of Life' API
R-cran-samr
GNU R significance analysis of microarrays
R-cran-sctransform
Variance Stabilizing Transformations for Single Cell UMI Data
R-cran-seqinr
GNU R biological sequences retrieval and analysis
R-cran-seurat
Tools for Single Cell Genomics
R-cran-tsne
t-distributed stochastic neighbor embedding for R (t-SNE)
R-cran-vegan
Community Ecology Package for R
R-cran-webgestaltr
find over-represented properties in gene lists
Ruby-bio
Ruby tools for computational molecular biology
Ruby-crb-blast
Run conditional reciprocal best blast
Sbmltoolbox
libsbml toolbox for octave and matlab
Snakemake
pythonic workflow management system
Toil
cross-platform workflow engine

Official Debian packages with lower relevance

Conda-package-handling
create and extract conda packages of various formats
Ctdconverter
Convert CTD files into Galaxy tool and CWL CommandLineTool files
Cthreadpool-dev
minimal ANSI C thread pool - development files
Cwlformat
code formatter for Common Workflow Language
Libargs-dev
simple header-only C++ argument parser library
Libbam-dev
manipulates nucleotide sequence alignments in BAM or SAM format
Libbbhash-dev
bloom-filter based minimal perfect hash function library
Libconcurrentqueue-dev
industrial-strength lock-free queue for C++
Libdisorder-dev
library for entropy measurement of byte streams (devel)
Libfreecontact-dev
fast protein contact predictor library - development files
Libfreecontact-doc
documentation for libfreecontact
Libfreecontact-perl
fast protein contact predictor - binding for Perl
Libmaus2-dev
collection of data structures and algorithms for biobambam (devel)
Libmilib-java
library for Next Generation Sequencing (NGS) data processing
Libminimap-dev
development headers for libminimap
Libmodhmm-dev
library for constructing, training and scoring hidden Markov models (dev)
Libpbcopper-dev
data structures, algorithms, and utilities for C++ applications -- header files
Librostlab-blast-doc
very fast C++ library for parsing the output of NCBI BLAST programs (doc)
Librostlab-doc
C++ library for computational biology (documentation)
Libsuma-dev
headers and static library for sumatra and sumaclust
Libsvmloc-dev
PSORTb adapted library for svm machine-learning library (dev)
Libtfbs-perl
scanning DNA sequence with a position weight matrix
Libxxsds-dynamic-dev
succinct and compressed fully-dynamic data structures library
Python-biopython-doc
Documentation for the Biopython library
Python3-alignlib
edit and Hamming distances for biological sequences
Python3-bel-resources
Python3 utilities for BEL resource files
Python3-biopython-sql
Biopython support for the BioSQL database schema (Python 3)
Python3-cogent3
framework for genomic biology
Python3-ctdopts
Gives your Python tools a CTD-compatible interface
Python3-intake
lightweight package for finding and investigating data
Python3-joypy
ridgeline-/joyplots plotting routine
Python3-ncls
datastructure for interval overlap queries
Python3-networkx
tool to create, manipulate and study complex networks (Python3)
Python3-pycosat
Python bindings to picosat
Python3-pyflow
lightweight parallel task engine for Python
Q2-alignment
QIIME 2 plugin for generating and manipulating alignments
Q2-cutadapt
QIIME 2 plugin to work with adapters in sequence data
Q2-dada2
QIIME 2 plugin to work with adapters in sequence data
Q2-demux
QIIME 2 plugin for demultiplexing of sequence reads
Q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
Q2-feature-table
QIIME 2 plugin supporting operations on feature tables
Q2-metadata
QIIME 2 plugin for working with and visualizing Metadata
Q2-quality-control
QIIME 2 plugin for quality assurance of feature and sequence data
Q2-quality-filter
QIIME2 plugin for PHRED-based filtering and trimming
Q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data
Q2-taxa
QIIME 2 plugin for working with feature taxonomy annotations
Q2-types
QIIME 2 plugin defining types for microbiome analysis
Q2cli
Click-based command line interface for QIIME 2
Q2templates
Design template package for QIIME 2 Plugins
Qiime
Quantitative Insights Into Microbial Ecology
R-bioc-affxparser
Affymetrix File Parsing SDK
R-bioc-affy
BioConductor methods for Affymetrix Oligonucleotide Arrays
R-bioc-affyio
BioConductor tools for parsing Affymetrix data files
R-bioc-altcdfenvs
BioConductor alternative CDF environments
R-bioc-annotate
BioConductor annotation for microarrays
R-bioc-annotationdbi
GNU R Annotation Database Interface for BioConductor
R-bioc-annotationhub
GNU R client to access AnnotationHub resources
R-bioc-aroma.light
BioConductor methods normalization and visualization of microarray data
R-bioc-arrayexpress
access to the ArrayExpress Microarray Database at EBI
R-bioc-biocgenerics
generic functions for Bioconductor
R-bioc-biocneighbors
Nearest Neighbor Detection for Bioconductor Packages
R-bioc-biomart
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
R-bioc-biomformat
GNU R interface package for the BIOM file format
R-bioc-biostrings
GNU R string objects representing biological sequences
R-bioc-biovizbase
GNU R basic graphic utilities for visualization of genomic data
R-bioc-bitseq
transcript expression inference and analysis for RNA-seq data
R-bioc-bsgenome
BioConductor infrastructure for Biostrings-based genome data packages
R-bioc-cner
CNE Detection and Visualization
R-bioc-complexheatmap
make complex heatmaps using GNU R
R-bioc-ctc
Cluster and Tree Conversion
R-bioc-cummerbund
tool for analysis of Cufflinks RNA-Seq output
R-bioc-dada2
sample inference from amplicon sequencing data
R-bioc-deseq
GNU R differential gene expression analysis
R-bioc-deseq2
R package for RNA-Seq Differential Expression Analysis
R-bioc-dnacopy
R package: DNA copy number data analysis
R-bioc-ebseq
R package for RNA-Seq Differential Expression Analysis
R-bioc-ensembldb
GNU R utilities to create and use an Ensembl based annotation database
R-bioc-genefilter
methods for filtering genes from microarray experiments
R-bioc-geneplotter
R package of functions for plotting genomic data
R-bioc-genomeinfodb
BioConductor utilities for manipulating chromosome identifiers
R-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
R-bioc-genomicfeatures
GNU R tools for making and manipulating transcript centric annotations
R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
R-bioc-geoquery
Get data from NCBI Gene Expression Omnibus (GEO)
R-bioc-go.db
annotation maps describing the entire Gene Ontology
R-bioc-graph
handle graph data structures for BioConductor
R-bioc-gseabase
Gene set enrichment data structures and methods
R-bioc-gsva
Gene Set Variation Analysis for microarray and RNA-seq data
R-bioc-gviz
Plotting data and annotation information along genomic coordinates
R-bioc-hypergraph
BioConductor hypergraph data structures
R-bioc-impute
Imputation for microarray data
R-bioc-iranges
GNU R low-level containers for storing sets of integer ranges
R-bioc-limma
linear models for microarray data
R-bioc-makecdfenv
BioConductor CDF Environment Maker
R-bioc-mergeomics
Integrative network analysis of omics data
R-bioc-metagenomeseq
GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-mofa
Multi-Omics Factor Analysis (MOFA)
R-bioc-multiassayexperiment
Software for integrating multi-omics experiments in BioConductor
R-bioc-nanostringqcpro
processing and QA for NanoString mRNA expression data
R-bioc-oligo
Preprocessing tools for oligonucleotide arrays
R-bioc-oligoclasses
Classes for high-throughput arrays supported by oligo and crlmm
R-bioc-org.hs.eg.db
genome-wide annotation for Human
R-bioc-pcamethods
BioConductor collection of PCA methods
R-bioc-phyloseq
GNU R handling and analysis of high-throughput microbiome census data
R-bioc-preprocesscore
BioConductor collection of pre-processing functions
R-bioc-purecn
copy number calling and SNV classification using targeted short read sequencing
R-bioc-qusage
qusage: Quantitative Set Analysis for Gene Expression
R-bioc-rbgl
R interface to the graph algorithms contained in the BOOST library
R-bioc-rsamtools
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
R-bioc-rtracklayer
GNU R interface to genome browsers and their annotation tracks
R-bioc-s4vectors
BioConductor S4 implementation of vectors and lists
R-bioc-savr
GNU R parse and analyze Illumina SAV files
R-bioc-shortread
GNU R classes and methods for high-throughput short-read sequencing data
R-bioc-snpstats
BioConductor SnpMatrix and XSnpMatrix classes and methods
R-bioc-structuralvariantannotation
Variant annotations for structural variants
R-bioc-tfbstools
GNU R Transcription Factor Binding Site (TFBS) Analysis
R-bioc-titancna
Subclonal copy number and LOH prediction from whole genome sequencing
R-bioc-tximport
transcript-level estimates for biological sequencing
R-bioc-variantannotation
BioConductor annotation of genetic variants
R-bioc-xvector
BioConductor representation and manpulation of external sequences
R-cran-adegenet
GNU R exploratory analysis of genetic and genomic data
R-cran-adephylo
GNU R exploratory analyses for the phylogenetic comparative method
R-cran-amap
Another Multidimensional Analysis Package
R-cran-biwt
biweight mean vector and covariance and correlation
R-cran-dt
GNU R wrapper of the JavaScript library 'DataTables'
R-cran-dynamictreecut
Methods for Detection of Clusters in Hierarchical Clustering
R-cran-fastcluster
Fast hierarchical clustering routines for GNU R
R-cran-future.apply
apply function to elements in parallel using futures
R-cran-future.batchtools
Future API for Parallel and Distributed Processing
R-cran-ica
Independent Component Analysis
R-cran-itertools
Iterator Tools
R-cran-kaos
Encoding of Sequences Based on Frequency Matrix Chaos
R-cran-metap
Meta-Analysis of Significance Values
R-cran-minerva
Maximal Information-Based Nonparametric Exploration
R-cran-natserv
GNU R 'NatureServe' Interface
R-cran-nmf
GNU R framework to perform non-negative matrix factorization
R-cran-optimalcutpoints
Computing Optimal Cutpoints in Diagnostic Tests
R-cran-parmigene
Parallel Mutual Information to establish Gene Networks
R-cran-pcapp
Robust PCA by Projection Pursuit
R-cran-proc
Display and Analyze ROC Curves
R-cran-rann
Fast Nearest Neighbour Search Using L2 Metric
R-cran-rcpphnsw
R bindings for a Library for Approximate Nearest Neighbors
R-cran-robustrankaggreg
Methods for robust rank aggregation
R-cran-rocr
GNU R package to prepare and display ROC curves
R-cran-rook
web server interface for R
R-cran-rsgcc
Gini correlation and clustering of gene expression data
R-cran-rsvd
Randomized Singular Value Decomposition
R-cran-shazam
Immunoglobulin Somatic Hypermutation Analysis
R-cran-sitmo
GNU R parallel pseudo random number generator 'sitmo' header files
R-cran-venndiagram
Generate High-Resolution Venn and Euler Plots
Ruby-rgfa
parse, edit and write GFA format graphs in Ruby

Debian packages in contrib or non-free

Python3-bcbio
library for analysing high-throughput sequencing data
Python3-seqcluster
analysis of small RNA in NGS data
Vdjtools
framework for post-analysis of B/T cell repertoires

Packaging has started and developers might try the packaging code in VCS

Libatomicqueue-dev
devel files for C++ atomic_queue library
Libfast-perl
FAST Analysis of Sequences Toolbox
Libforester-java
Libraries for evolutionary biology and comparative genomics research
Libgoby-java
store next-generation sequencing data and intermediary analysis results
Libnexml-java
Java API for NeXML
Libqcpp-dev
C++11 library for NGS data quality control -- headers
Libroadrunner-dev
simulation engine for systems and synthetic biology (development)
Libssu-dev
de facto repository for high-performance phylogenetic diversity calculations (dev)
Libswarm2-dev
agent-based modeling to education, biomedical research and others
Python3-consensuscore2
generate consensus sequences for PacBio data -- Python 3
Python3-galaxy-lib
Subset of Galaxy core code base designed to be used
Python3-misopy
Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
Python3-roadrunner
Python 3 bindings for libroadrunner
Python3-scanpy
Single-Cell Analysis in Python
Python3-unifrac
de facto repository for high-performance phylogenetic diversity calculations
Q2-fragment-insertion
QIIME 2 plugin for fragment insertion
Q2-vsearch
QIIME 2 plugin for clustering and dereplicating with vsearch
R-bioc-bridgedbr
identifier mapping between biological databases
R-cran-drinsight
drug repurposing on transcriptome sequencing data
R-other-apmswapp
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
R-other-hms-dbmi-spp
GNU R ChIP-seq processing pipeline

No known packages available

Bioclipse
platform for chemo- and bioinformatics based on Eclipse
Octace-bioinfo
Bioinformatics manipulation for Octave

Next generation sequencing - Debian Med bioinformatics applications usable in Next Generation Sequencing

It aims at gettting packages which specialize in the processing or interpretation of data generated with next- (and later-) generation high-thoughput sequencing technologies.

Official Debian packages with high relevance

Anfo
Short Read Aligner/Mapper from MPG
Arden
specificity control for read alignments using an artificial reference
Art-nextgen-simulation-tools
simulation tools to generate synthetic next-generation sequencing reads
Artfastqgenerator
outputs artificial FASTQ files derived from a reference genome
Bamtools
toolkit for manipulating BAM (genome alignment) files
Bcftools
genomic variant calling and manipulation of VCF/BCF files
Bedtools
suite of utilities for comparing genomic features
Berkeley-express
Streaming quantification for high-throughput sequencing
Bio-rainbow
clustering and assembling short reads for bioinformatics
Blasr
mapping single-molecule sequencing reads
Bowtie
Ultrafast memory-efficient short read aligner
Bowtie2
ultrafast memory-efficient short read aligner
Bwa
Burrows-Wheeler Aligner
Canu
single molecule sequence assembler for genomes
Changeo
Repertoire clonal assignment toolkit (Python 3)
Crac
integrated RNA-Seq read analysis
Cutadapt
Clean biological sequences from high-throughput sequencing reads
Daligner
local alignment discovery between long nucleotide sequencing reads
Deepnano
alternative basecaller for MinION reads of genomic sequences
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Dnaclust
tool for clustering millions of short DNA sequences
Dwgsim
short sequencing read simulator
Ea-utils
command-line tools for processing biological sequencing data
Fastaq
FASTA and FASTQ file manipulation tools
Fastp
Ultra-fast all-in-one FASTQ preprocessor
Fastqc
quality control for high throughput sequence data
Flexbar
flexible barcode and adapter removal for sequencing platforms
Fml-asm
tool for assembling Illumina short reads in small regions
Fsm-lite
frequency-based string mining (lite)
Giira
RNA-Seq driven gene finding incorporating ambiguous reads
Grinder
Versatile omics shotgun and amplicon sequencing read simulator
Hilive
realtime alignment of Illumina reads
Hinge
long read genome assembler based on hinging
Hisat2
graph-based alignment of short nucleotide reads to many genomes
Idba
iterative De Bruijn Graph short read assemblers
Igdiscover
analyzes antibody repertoires to find new V genes
Igor
infers V(D)J recombination processes from sequencing data
Iva
iterative virus sequence assembler
Khmer
in-memory DNA sequence kmer counting, filtering & graph traversal
Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
Kraken
assigning taxonomic labels to short DNA sequences
Kraken2
taxonomic classification system using exact k-mer matches
Last-align
genome-scale comparison of biological sequences
Libvcflib-tools
C++ library for parsing and manipulating VCF files (tools)
Macs
Model-based Analysis of ChIP-Seq on short reads sequencers
Mapdamage
tracking and quantifying damage patterns in ancient DNA sequences
Mapsembler2
bioinformatics targeted assembly software
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Maqview
graphical read alignment viewer for short gene sequences
Mhap
locality-sensitive hashing to detect long-read overlaps
Microbiomeutil
Microbiome Analysis Utilities
Mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
Mothur
sequence analysis suite for research on microbiota
Nanopolish
consensus caller for nanopore sequencing data
Paleomix
pipelines and tools for the processing of ancient and modern HTS data
Pbhoney
genomic structural variation discovery
Pbjelly
genome assembly upgrading tool
Pbsuite
software for Pacific Biosciences sequencing data
Picard-tools
Command line tools to manipulate SAM and BAM files
Pirs
Profile based Illumina pair-end Reads Simulator
Pizzly
Identifies gene fusions in RNA sequencing data
Placnet
Plasmid Constellation Network project
Poretools
toolkit for nanopore nucleotide sequencing data
Python3-airr
Data Representation Standard library for antibody and TCR sequences
Python3-gffutils
Work with GFF and GTF files in a flexible database framework
Python3-presto
toolkit for processing B and T cell sequences (Python3 module)
Python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
Python3-sqt
SeQuencing Tools for biological DNA/RNA high-throughput data
Qcumber
quality control of genomic sequences
Qiime
Quantitative Insights Into Microbial Ecology
Quorum
QUality Optimized Reads of genomic sequences
R-bioc-deseq2
R package for RNA-Seq Differential Expression Analysis
R-bioc-edger
Empirical analysis of digital gene expression data in R
R-bioc-hilbertvis
GNU R package to visualise long vector data
R-bioc-metagenomeseq
GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-rsubread
Subread Sequence Alignment and Counting for R
R-cran-alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-shazam
Immunoglobulin Somatic Hypermutation Analysis
R-cran-tcr
Advanced Data Analysis of Immune Receptor Repertoires
R-cran-tigger
Infers new Immunoglobulin alleles from Rep-Seq Data
Rna-star
ultrafast universal RNA-seq aligner
Rtax
Classification of sequence reads of 16S ribosomal RNA gene
Salmon
wicked-fast transcript quantification from RNA-seq data
Sambamba
tools for working with SAM/BAM data
Samblaster
marks duplicates, extracts discordant/split reads
Samtools
processing sequence alignments in SAM, BAM and CRAM formats
Scoary
pangenome-wide association studies
Scythe
Bayesian adaptor trimmer for sequencing reads
Seqprep
stripping adaptors and/or merging paired reads of DNA sequences with overlap
Seqtk
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sga
de novo genome assembler that uses string graphs
Sickle
windowed adaptive trimming tool for FASTQ files using quality
Smalt
Sequence Mapping and Alignment Tool
Smrtanalysis
software suite for single molecule, real-time sequencing
Snap-aligner
Scalable Nucleotide Alignment Program
Sniffles
structural variation caller using third-generation sequencing
Snp-sites
Binary code for the package snp-sites
Snpomatic
fast, stringent short-read mapping software
Soapdenovo
short-read assembly method to build de novo draft assembly
Soapdenovo2
short-read assembly method to build de novo draft assembly
Sortmerna
tool for filtering, mapping and OTU-picking NGS reads
Spades
genome assembler for single-cell and isolates data sets
Sprai
single-pass sequencing read accuracy improver
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Srst2
Short Read Sequence Typing for Bacterial Pathogens
Ssake
genomics application for assembling millions of very short DNA sequences
Stacks
pipeline for building loci from short-read DNA sequences
Stringtie
assemble short RNAseq reads to transcripts
Subread
toolkit for processing next-gen sequencing data
Sumaclust
fast and exact clustering of genomic sequences
Sumatra
fast and exact comparison and clustering of sequences
Tabix
generic indexer for TAB-delimited genome position files
Transrate-tools
helper for transrate
Trimmomatic
flexible read trimming tool for Illumina NGS data
Trinityrnaseq
RNA-Seq De novo Assembly
Uc-echo
error correction algorithm designed for short-reads from NGS
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads
Velvet-long
Nucleic acid sequence assembler for very short reads, long version
Velvetoptimiser
automatically optimise Velvet do novo assembly parameters
Vsearch
tool for processing metagenomic sequences
Wham-align
Wisconsin's High-Throughput Alignment Method
Wigeon
reimplementation of the Pintail 16S DNA anomaly detection utility

Official Debian packages with lower relevance

Nanolyse
remove lambda phage reads from a fastq file
Python3-anndata
annotated gene by sample numpy matrix

Debian packages in contrib or non-free

Bcbio
toolkit for analysing high-throughput sequencing data
Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
Igv
Integrative Genomics Viewer
Vdjtools
framework for post-analysis of B/T cell repertoires

Packaging has started and developers might try the packaging code in VCS

Graphmap2
highly sensitive and accurate mapper for long, error-prone reads
Mosaik-aligner
reference-guided aligner for next-generation sequencing
Nanoplot
plotting scripts for long read sequencing data
Umap
quantify genome and methylome mappability

No known packages available

Annovar
annotate genetic variants detected from diverse genomes
Forge
genome assembler for mixed read types

Phylogeny - Debian Med phylogeny packages

This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software.

Official Debian packages with high relevance

Altree
program to perform phylogeny-based association and localization analysis
Beast-mcmc
Bayesian MCMC phylogenetic inference
Clustalw
global multiple nucleotide or peptide sequence alignment
Clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Exonerate
generic tool for pairwise sequence comparison
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Figtree
graphical phylogenetic tree viewer
Gmap
spliced and SNP-tolerant alignment for mRNA and short reads
Hmmer
profile hidden Markov models for protein sequence analysis
Iqtree
efficient phylogenetic software by maximum likelihood
Jmodeltest
HPC selection of models of nucleotide substitution
Kalign
Global and progressive multiple sequence alignment
Mrbayes
Bayesian Inference of Phylogeny
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Njplot
phylogenetic tree drawing program
Phylip
package of programs for inferring phylogenies
Phyml
Phylogenetic estimation using Maximum Likelihood
Poa
Partial Order Alignment for multiple sequence alignment
Populations
population genetic software
Pplacer
phylogenetic placement and downstream analysis
Proalign
Probabilistic multiple alignment program
Probalign
multiple sequence alignment using partition function posterior probabilities
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prottest
selection of best-fit models of protein evolution
Quicktree
Neighbor-Joining algorithm for phylogenies
Seaview
Multiplatform interface for sequence alignment and phylogeny
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Spread-phy
analyze and visualize phylogeographic reconstructions
T-coffee
Multiple Sequence Alignment
Tm-align
structural alignment of proteins
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Treeview
Java re-implementation of Michael Eisen's TreeView
Treeviewx
Displays and prints phylogenetic trees

Official Debian packages with lower relevance

Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)

Packaging has started and developers might try the packaging code in VCS

Forester
Graphical vizualiation tool Archaeopteryx
Patristic
Calculate patristic distances and comparing the components of genetic change

No known packages available but some record of interest (WNPP bug)

Phylowin
Graphical interface for molecular phylogenetic inference

No known packages available

Gbioseq
DNA sequence editor for Linux
Jstreeview
Editor for Phylogenetic Trees
Phpphylotree
draw phylogenetic trees
Treetime
Bayesian sampling of phylogenetic trees from molecular data

Cloud - Debian Med bioinformatics applications usable in cloud computing

This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.

Official Debian packages with high relevance

Abyss
de novo, parallel, sequence assembler for short reads
Acedb-other
retrieval of DNA or protein sequences
Aevol
digital genetics model to run Evolution Experiments in silico
Alien-hunter
Interpolated Variable Order Motifs to identify horizontally acquired DNA
Altree
program to perform phylogeny-based association and localization analysis
Amap-align
Protein multiple alignment by sequence annealing
Ampliconnoise
removal of noise from 454 sequenced PCR amplicons
Anfo
Short Read Aligner/Mapper from MPG
Aragorn
tRNA and tmRNA detection in nucleotide sequences
Arden
specificity control for read alignments using an artificial reference
Autodock
analysis of ligand binding to protein structure
Autodock-vina
docking of small molecules to proteins
Autogrid
pre-calculate binding of ligands to their receptor
Bamtools
toolkit for manipulating BAM (genome alignment) files
Bedtools
suite of utilities for comparing genomic features
Bioperl
Perl tools for computational molecular biology
Bioperl-run
BioPerl wrappers: scripts
Biosquid
utilities for biological sequence analysis
Blast2
transitional dummy package to ncbi-blast+-legacy
Bowtie
Ultrafast memory-efficient short read aligner
Bowtie2
ultrafast memory-efficient short read aligner
Boxshade
Pretty-printing of multiple sequence alignments
Bwa
Burrows-Wheeler Aligner
Cassiopee
index and search tool in genomic sequences
Cd-hit
suite of programs designed to quickly group sequences
Cdbfasta
Constant DataBase indexing and retrieval tools for multi-FASTA files
Circos
plotter for visualizing data
Clearcut
extremely efficient phylogenetic tree reconstruction
Clonalframe
inference of bacterial microevolution using multilocus sequence data
Clustalo
General-purpose multiple sequence alignment program for proteins
Clustalw
global multiple nucleotide or peptide sequence alignment
Concavity
predictor of protein ligand binding sites from structure and conservation
Conservation-code
protein sequence conservation scoring tool
Datamash
statistics tool for command-line interface
Dialign
Segment-based multiple sequence alignment
Dialign-tx
Segment-based multiple sequence alignment
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder
cysteines disulfide bonding state and connectivity predictor
Dnaclust
tool for clustering millions of short DNA sequences
Dssp
protein secondary structure assignment based on 3D structure
Embassy-domainatrix
Extra EMBOSS commands to handle domain classification file
Embassy-domalign
Extra EMBOSS commands for protein domain alignment
Embassy-domsearch
Extra EMBOSS commands to search for protein domains
Emboss
European molecular biology open software suite
Exonerate
generic tool for pairwise sequence comparison
Fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
Fastlink
faster version of pedigree programs of Linkage
Fastqc
quality control for high throughput sequence data
Fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
Fitgcp
fitting genome coverage distributions with mixture models
Flexbar
flexible barcode and adapter removal for sequencing platforms
Freecontact
fast protein contact predictor
Gasic
genome abundance similarity correction
Genometools
versatile genome analysis toolkit
Gff2aplot
pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps
produces PostScript graphical output from GFF-files
Giira
RNA-Seq driven gene finding incorporating ambiguous reads
Glam2
gapped protein motifs from unaligned sequences
Gmap
spliced and SNP-tolerant alignment for mRNA and short reads
Grinder
Versatile omics shotgun and amplicon sequencing read simulator
Gromacs
Molecular dynamics simulator, with building and analysis tools
Hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
Hisat2
graph-based alignment of short nucleotide reads to many genomes
Hmmer
profile hidden Markov models for protein sequence analysis
Idba
iterative De Bruijn Graph short read assemblers
Infernal
inference of RNA secondary structural alignments
Jellyfish
count k-mers in DNA sequences
Kalign
Global and progressive multiple sequence alignment
Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
Last-align
genome-scale comparison of biological sequences
Loki
MCMC linkage analysis on general pedigrees
Macs
Model-based Analysis of ChIP-Seq on short reads sequencers
Mafft
Multiple alignment program for amino acid or nucleotide sequences
Mapsembler2
bioinformatics targeted assembly software
Maq
maps short fixed-length polymorphic DNA sequence reads to reference sequences
Melting
compute the melting temperature of nucleic acid duplex
Minia
short-read biological sequence assembler
Mipe
Tools to store PCR-derived data
Mira-assembler
Whole Genome Shotgun and EST Sequence Assembler
Mlv-smile
Find statistically significant patterns in sequences
Mothur
sequence analysis suite for research on microbiota
Mrbayes
Bayesian Inference of Phylogeny
Mummer
Efficient sequence alignment of full genomes
Muscle
Multiple alignment program of protein sequences
Mustang
multiple structural alignment of proteins
Ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-tools-bin
NCBI libraries for biology applications (text-based utilities)
Ncoils
coiled coil secondary structure prediction
Neobio
computes alignments of amino acid and nucleotide sequences
Paraclu
Parametric clustering of genomic and transcriptomic features
Parsinsert
Parsimonious Insertion of unclassified sequences into phylogenetic trees
Pdb2pqr
Preparation of protein structures for electrostatics calculations
Perm
efficient mapping of short reads with periodic spaced seeds
Phyml
Phylogenetic estimation using Maximum Likelihood
Phyutility
simple analyses or modifications on both phylogenetic trees and data matrices
Picard-tools
Command line tools to manipulate SAM and BAM files
Plink
whole-genome association analysis toolset
Plink1.9
whole-genome association analysis toolset
Plink2
whole-genome association analysis toolset
Poa
Partial Order Alignment for multiple sequence alignment
Prank
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Prime-phylo
bayesian estimation of gene trees taking the species tree into account
Primer3
tool to design flanking oligo nucleotides for DNA amplification
Probabel
Toolset for Genome-Wide Association Analysis
Probcons
PROBabilistic CONSistency-based multiple sequence alignment
Proda
multiple alignment of protein sequences
Prodigal
Microbial (bacterial and archaeal) gene finding program
Python3-biomaj3-cli
BioMAJ client
Python3-biopython
Python3 library for bioinformatics
Python3-cogent3
framework for genomic biology
Qiime
Quantitative Insights Into Microbial Ecology
R-bioc-edger
Empirical analysis of digital gene expression data in R
R-bioc-hilbertvis
GNU R package to visualise long vector data
R-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-qtl
GNU R package for genetic marker linkage analysis
R-cran-vegan
Community Ecology Package for R
R-other-mott-happy.hbrem
GNU R package for fine-mapping complex diseases
Raster3d
tools for generating images of proteins or other molecules
Readseq
Conversion between sequence formats
Rnahybrid
Fast and effective prediction of microRNA/target duplexes
Rtax
Classification of sequence reads of 16S ribosomal RNA gene
Samtools
processing sequence alignments in SAM, BAM and CRAM formats
Seqan-apps
C++ library for the analysis of biological sequences
Sibsim4
align expressed RNA sequences on a DNA template
Sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
Sim4
tool for aligning cDNA and genomic DNA
Smalt
Sequence Mapping and Alignment Tool
Snap
location of genes from DNA sequence with hidden markov model
Soapdenovo
short-read assembly method to build de novo draft assembly
Soapdenovo2
short-read assembly method to build de novo draft assembly
Squizz
Converter for genetic sequences and alignments
Sra-toolkit
utilities for the NCBI Sequence Read Archive
Ssake
genomics application for assembling millions of very short DNA sequences
Staden-io-lib-utils
programs for manipulating DNA sequencing files
T-coffee
Multiple Sequence Alignment
Tabix
generic indexer for TAB-delimited genome position files
Theseus
superimpose macromolecules using maximum likelihood
Tigr-glimmer
Gene detection in archea and bacteria
Tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
Vcftools
Collection of tools to work with VCF files
Velvet
Nucleic acid sequence assembler for very short reads
Wise
comparison of biopolymers, like DNA and protein sequences
Zalign
parallel local alignment of biological sequences

Debian packages in contrib or non-free

Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip
EMBOSS conversions of the programs in the phylip package

Packaging has started and developers might try the packaging code in VCS

Bagpipe
genomewide LD mapping

Content management - Debian Med content management systems

Here you can find software that is useful to build a content management system for medical care.

Packaging has started and developers might try the packaging code in VCS

Xnat
platform for data management and productivity tasks in neuroimaging
Zope-zms
Content management for science, technology and medicine

No known packages available

Hid
database management system for clinical imaging

Covid-19 - This task exists only for tagging COVID-19 relevant cases

The Debian Med team intends to take part at the

 COVID-19 Biohackathon (April 5-11, 2020)
This task was created only for the purpose to list relevant packages.

Official Debian packages with high relevance

Abacas
close gaps in genomic alignments from short reads
Abyss
de novo, parallel, sequence assembler for short reads
Aeskulap
medical image viewer and DICOM network client
Allelecount
NGS copy number algorithms
Assembly-stats
get assembly statistics from FASTA and FASTQ files
Augur
pipeline components for real-time virus analysis
Bamclipper
Remove gene-specific primer sequences from SAM/BAM alignments
Bamkit
tools for common BAM file manipulations
Bbmap
short read aligner and other bioinformatic tools
Bcalm
de Bruijn compaction in low memory
Bcftools
genomic variant calling and manipulation of VCF/BCF files
Bedtools
suite of utilities for comparing genomic features
Biobambam2
tools for early stage alignment file processing
Bowtie2
ultrafast memory-efficient short read aligner
Busco
benchmarking sets of universal single-copy orthologs
Bustools
program for manipulating BUS files for single cell RNA-Seq datasets
Bwa
Burrows-Wheeler Aligner
Cat-bat
taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Centrifuge
rapid and memory-efficient system for classification of DNA sequences
Changeo
Repertoire clonal assignment toolkit (Python 3)
Chip-seq
tools performing common ChIP-Seq data analysis tasks
Clonalframeml
Efficient Inference of Recombination in Whole Bacterial Genomes
Conquest-common
ConQuest DICOM Server - common files
Cutadapt
Clean biological sequences from high-throughput sequencing reads
Cwltool
Common Workflow Language reference implementation
Dcmtk
OFFIS DICOM toolkit command line utilities
Delly
Structural variant discovery by read analysis
Dextractor
(d)extractor and compression command library
Diamond-aligner
accelerated BLAST compatible local sequence aligner
Discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Drop-seq-tools
analyzing Drop-seq data
Epigrass
scientific tool for simulations and scenario analysis in network epidemiology
Fasta3
tools for searching collections of biological sequences
Fastp
Ultra-fast all-in-one FASTQ preprocessor
Fastqc
quality control for high throughput sequence data
Filtlong
quality filtering tool for long reads of genome sequences
Flash
Fast Length Adjustment of SHort reads
Freebayes
Bayesian haplotype-based polymorphism discovery and genotyping
Genometools
versatile genome analysis toolkit
Gffread
GFF/GTF format conversions, region filtering, FASTA sequence extraction
Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
Gnumed-client
medical practice management - Client
Gnumed-server
medical practice management - server
Gromacs
Molecular dynamics simulator, with building and analysis tools
Gubbins
phylogenetic analysis of genome sequences
Imagej
Image processing program with a focus on microscopy images
Ivar
functions broadly useful for viral amplicon-based sequencing
Kalign
Global and progressive multiple sequence alignment
Kallisto
near-optimal RNA-Seq quantification
Kraken2
taxonomic classification system using exact k-mer matches
Lastz
pairwise aligning DNA sequences
Libbbhash-dev
bloom-filter based minimal perfect hash function library
Libchipcard-dev
API for smartcard readers
Libgclib-dev
header files for Genome Code Lib (GCLib)
Libgdcm-tools
Grassroots DICOM tools and utilities
Libhtscodecs-dev
Development headers for custom compression for CRAM and others
Libics-dev
Image Cytometry Standard file reading and writing (devel)
Libmaus2-dev
collection of data structures and algorithms for biobambam (devel)
Libmilib-java
library for Next Generation Sequencing (NGS) data processing
Libseqan3-dev
C++ library for the analysis of biological sequences v3 (development)
Lighter
fast and memory-efficient sequencing error corrector
Lumpy-sv
general probabilistic framework for structural variant discovery
Mecat2
ultra-fast and accurate de novo assembly tools for SMRT reads
Megahit
ultra-fast and memory-efficient meta-genome assembler
Metabat
robust statistical framework for reconstructing genomes from metagenomic data
Minia
short-read biological sequence assembler
Minimap2
versatile pairwise aligner for genomic and spliced nucleotide sequences
Mmb
model the structure and dynamics of macromolecules
Mmseqs2
ultra fast and sensitive protein search and clustering
Multiqc
output integration for RNA sequencing across tools and samples
Muscle
Multiple alignment program of protein sequences
Nanofilt
filtering and trimming of long read sequencing data
Nanolyse
remove lambda phage reads from a fastq file
Nanook
pre- and post-alignment analysis of nanopore sequencing data
Nanopolish
consensus caller for nanopore sequencing data
Nanosv
structural variant caller for nanopore data
Ncbi-blast+
next generation suite of BLAST sequence search tools
Ngmlr
CoNvex Gap-cost alignMents for Long Reads
Nthash
Methods to evaluate runtime and uniformity tests for hashing methods
Odil
C++11 library for the DICOM standard (application)
Orthanc
Lightweight, RESTful DICOM server for medical imaging
Orthanc-dicomweb
Plugin to extend Orthanc with support of WADO and DICOMweb
Orthanc-python
Develop plugins for Orthanc using the Python programming language
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Paleomix
pipelines and tools for the processing of ancient and modern HTS data
Parallel-fastq-dump
parallel fastq-dump wrapper
Parasail
Aligner based on libparasail3
Picard-tools
Command line tools to manipulate SAM and BAM files
Picopore
lossless compression of Nanopore files
Pigx-rnaseq
pipeline for checkpointed and distributed RNA-seq analyses
Pinfish
Collection of tools to annotate genomes using long read transcriptomics data
Plasmidid
mapping-based, assembly-assisted plasmid identification tool
Plink1.9
whole-genome association analysis toolset
Plink2
whole-genome association analysis toolset
Plip
fully automated protein-ligand interaction profiler
Porechop
adapter trimmer for Oxford Nanopore reads
Poretools
toolkit for nanopore nucleotide sequencing data
Pplacer
phylogenetic placement and downstream analysis
Presto
toolkit for processing B and T cell sequences
Prinseq-lite
PReprocessing and INformation of SEQuence data (lite version)
Prokka
rapid annotation of prokaryotic genomes
Proteinortho
Detection of (Co-)orthologs in large-scale protein analysis
Pybedtools-bin
Scripts produced for pybedtools
Pycoqc
computes metrics and generates Interactive QC plots
Pyomo
PYthon Optimization Modeling Objects
Python3-biom-format
Biological Observation Matrix (BIOM) format (Python 3)
Python3-biopython
Python3 library for bioinformatics
Python3-bx
library to manage genomic data and its alignment
Python3-cgecore
Python3 module for the Center for Genomic Epidemiology
Python3-cogent3
framework for genomic biology
Python3-cooler
library for a sparse, compressed, binary persistent storage
Python3-cyvcf2
VCF parser based on htslib (Python 3)
Python3-depinfo
retrieve and print Python 3 package dependencies
Python3-drmaa
interface to DRMAA-compliant distributed resource management systems
Python3-etelemetry
lightweight Python3 client to communicate with the etelemetry server
Python3-gffutils
Work with GFF and GTF files in a flexible database framework
Python3-htseq
Python3 high-throughput genome sequencing read analysis utilities
Python3-nanoget
extract information from Oxford Nanopore sequencing data and alignments
Python3-nanomath
simple math function for other Oxford Nanopore processing scripts
Python3-pairix
1D/2D indexing and querying with a pair of genomic coordinates
Python3-pairtools
Framework to process sequencing data from a Hi-C experiment
Python3-pauvre
QC and genome browser plotting Oxford Nanopore and PacBio long reads
Python3-pbcommand
common command-line interface for Pacific Biosciences analysis modules
Python3-pbcore
Python 3 library for processing PacBio data files
Python3-pyani
Python3 module for average nucleotide identity analyses
Python3-pychopper
identify, orient and trim full-length Nanopore cDNA reads
Python3-pydicom
DICOM medical file reading and writing (Python 3)
Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
Python3-pynn
simulator-independent specification of neuronal network models
Python3-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-questplus
QUEST+ implementation in Python3
Python3-scitrack
Python3 library to track scientific data
Python3-screed
short nucleotide read sequence utils in Python 3
Python3-seirsplus
Models of SEIRS epidemic dynamics with extensions
Python3-streamz
build pipelines to manage continuous streams of data
Python3-tinyalign
numerical representation of differences between strings
Python3-toolz
List processing tools and functional utilities
Python3-torch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
Python3-tornado
scalable, non-blocking web server and tools - Python 3 package
Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Python3-typed-ast
AST with PEP 484 type comments support
Python3-vcf
Variant Call Format (VCF) parser for Python 3
Q2-cutadapt
QIIME 2 plugin to work with adapters in sequence data
Q2-feature-table
QIIME 2 plugin supporting operations on feature tables
Q2-quality-filter
QIIME2 plugin for PHRED-based filtering and trimming
Qcat
demultiplexing Oxford Nanopore reads from FASTQ files
Quicktree
Neighbor-Joining algorithm for phylogenies
R-bioc-htsfilter
GNU R filter replicated high-throughput transcriptome sequencing data
R-bioc-limma
linear models for microarray data
R-bioc-mutationalpatterns
GNU R comprehensive genome-wide analysis of mutational processes
R-bioc-pwmenrich
PWM enrichment analysis
R-bioc-rgsepd
GNU R gene set enrichment / projection displays
R-bioc-rsamtools
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
R-bioc-tcgabiolinks
GNU R/Bioconductor package for integrative analysis with GDC data
R-cran-alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-covid19us
cases of COVID-19 in the United States prepared for GNU R
R-cran-diagnosismed
medical diagnostic test accuracy analysis toolkit
R-cran-epi
GNU R epidemiological analysis
R-cran-epibasix
GNU R Elementary Epidemiological Functions
R-cran-epicalc
GNU R Epidemiological calculator
R-cran-epiestim
GNU R estimate time varying reproduction numbers from rpidemic curves
R-cran-epir
GNU R Functions for analysing epidemiological data
R-cran-epitools
GNU R Epidemiology Tools for Data and Graphics
R-cran-hms
GNU R pretty time of day
R-cran-incidence
GNU R compute, handle, plot and model incidence of dated events
R-cran-lexrankr
extractive summarization of text with the LexRank algorithm
R-cran-mediana
clinical trial simulations
R-cran-msm
GNU R Multi-state Markov and hidden Markov models in continuous time
R-cran-qtl
GNU R package for genetic marker linkage analysis
R-cran-seroincidence
GNU R seroincidence calculator tool
R-cran-sf
Simple Features for R
R-cran-shazam
Immunoglobulin Somatic Hypermutation Analysis
R-cran-sjplot
GNU R data visualization for statistics in social science
R-cran-spp
GNU R ChIP-seq processing pipeline
R-cran-stringi
GNU R character string processing facilities
R-cran-surveillance
GNU R package for the Modeling and Monitoring of Epidemic Phenomena
R-cran-tigger
Infers new Immunoglobulin alleles from Rep-Seq Data
R-other-ascat
Allele-Specific Copy Number Analysis of Tumours
Ragout
Reference-Assisted Genome Ordering UTility
Readucks
Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
Recan
genetic distance plotting for recombination events analysis
Rna-star
ultrafast universal RNA-seq aligner
Rsem
RNA-Seq by Expectation-Maximization
Ruby-bio
Ruby tools for computational molecular biology
Salmon
wicked-fast transcript quantification from RNA-seq data
Samblaster
marks duplicates, extracts discordant/split reads
Samclip
filter SAM file for soft and hard clipped alignments
Samtools
processing sequence alignments in SAM, BAM and CRAM formats
Scrappie
basecaller for Nanopore sequencer
Sepp
phylogeny with ensembles of Hidden Markov Models
Seqkit
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Seqmagick
imagemagick-like frontend to Biopython SeqIO
Shapeit4
fast and accurate method for estimation of haplotypes (phasing)
Shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
Smrtanalysis
software suite for single molecule, real-time sequencing
Snakemake
pythonic workflow management system
Spades
genome assembler for single-cell and isolates data sets
Spaln
splicing-aware transcript-alignment to genomic DNA
Staden-io-lib-utils
programs for manipulating DNA sequencing files
Stringtie
assemble short RNAseq reads to transcripts
Sumaclust
fast and exact clustering of genomic sequences
Texlive-science
TeX Live: Mathematics, natural sciences, computer science packages
Thesias
Testing Haplotype Effects In Association Studies
Tiddit
structural variant calling
Tnseq-transit
statistical calculations of essentiality of genes or genomic regions
Toil
cross-platform workflow engine
Tombo
identification of modified nucleotides from raw nanopore sequencing data
Tophat-recondition
post-processor for TopHat unmapped reads
Trinculo
toolkit to carry out genetic association for multi-category phenotypes
Umap-learn
Uniform Manifold Approximation and Projection
Umis
tools for processing UMI RNA-tag data
Uncalled
Utility for Nanopore Current Alignment to Large Expanses of DNA
Unicycler
hybrid assembly pipeline for bacterial genomes
Vg
tools for working with genome variation graphs
Vsearch
tool for processing metagenomic sequences
Vt
toolset for short variant discovery in genetic sequence data
Workrave
Repetitive Strain Injury prevention tool
Wtdbg2
de novo sequence assembler for long noisy reads
Yanagiba
filter low quality Oxford Nanopore reads basecalled with Albacore
Yanosim
read simulator nanopore DRS datasets

Official Debian packages with lower relevance

Libsimde-dev
Implementations of SIMD instructions for all systems
Python3-anndata
annotated gene by sample numpy matrix
Python3-mmtf
binary encoding of biological structures (Python 3)
R-bioc-rsubread
Subread Sequence Alignment and Counting for R

Debian packages in contrib or non-free

Bcbio
toolkit for analysing high-throughput sequencing data
Python3-seqcluster
analysis of small RNA in NGS data
Varscan
variant detection in next-generation sequencing data
Vienna-rna
RNA sequence analysis

Debian packages in New queue (hopefully available soon)

Fastani
Fast alignment-free computation of whole-genome Average Nucleotide Identity
Snpeff
genetic variant annotation and effect prediction toolbox - tool

Packaging has started and developers might try the packaging code in VCS

Arvados
managing and analyzing biomedical big data
Auspice
web app for visualizing pathogen evolution
Blat
BLAST-like alignment tool
Chime
COVID-19 Hospital Impact Model for Epidemics
Covpipe
pipeline to generate consensus sequences from NGS reads
Ensembl-vep
Variant Effect Predictor predicting the functional effects of genomic variants
Fieldbioinformatics
pipeline with virus identification with Nanopore sequencer
Flappie
flip-flop basecaller for Oxford Nanopore reads
Flye
de novo assembler for single molecule sequencing reads using repeat graphs
Graphmap2
highly sensitive and accurate mapper for long, error-prone reads
Libtensorflow-framework2
Computation using data flow graphs for scalable machine learning
Manta
structural variant and indel caller for mapped sequencing data
Medaka
sequence correction provided by ONT Research
Nanoplot
plotting scripts for long read sequencing data
Ncbi-magicblast
RNA-seq mapping tool
Nextflow
DSL for data-driven computational pipelines
Nextstrain-ncov
Nextstrain build for novel coronavirus (nCoV)
Oncofuse
predicting oncogenic potential of gene fusions
Optitype
precision HLA typing from next-generation sequencing data
Pangolin
Phylogenetic Assignment of Named Global Outbreak LINeages
Pomoxis
analysis components from Oxford Nanopore Research
Python3-scanpy
Single-Cell Analysis in Python
Qualimap
evaluating next generation sequencing alignment data
Quast
Quality Assessment Tool for Genome Assemblies
R-bioc-rcpi
molecular informatics toolkit for compound-protein interaction in drug discovery
R-cran-covid19
GNU R Coronavirus COVID-19 data acquisition and visualization
R-other-fastbaps
A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
Rosa
Removal of Spurious Antisense in biological RNA sequences
Sailfish
RNA-seq expression estimation
Seqwish
alignment to variation graph inducer
Shiny-server
put Shiny web apps online
Signalalign
HMM-HDP models for MinION signal alignments
Streamlit
fast way to build custom ML tools
Strelka
strelka2 germline and somatic small variant caller
Ufasta
utility to manipulate fasta files
Vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

Medical data - Debian Med drug databases

This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application.

Official Debian packages with high relevance

Freediams
pharmaceutical drug prescription and interaction manager
Freemedforms-freedata
free extra-data for the FreeMedForms project
Python3-hl7
Python3 library for parsing HL7 messages

Official Debian packages with lower relevance

Oscar
Open Source CPAP Analysis Reporter (OSCAR)

No known packages available

Drugref.org
pharmaceutical reference database

Dental - Debian Med packages related to dental practice

This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice.

Official Debian packages with high relevance

Entangle
Tethered Camera Control & Capture
Imagetooth
library generating images of teeth for odontograms
Openmolar
dental practice management software

Epidemiology - Debian Med epidemiology related packages

This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf

Official Debian packages with high relevance

Epigrass
scientific tool for simulations and scenario analysis in network epidemiology
Python3-seirsplus
Models of SEIRS epidemic dynamics with extensions
Python3-torch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
R-cran-covid19us
cases of COVID-19 in the United States prepared for GNU R
R-cran-diagnosismed
medical diagnostic test accuracy analysis toolkit
R-cran-epi
GNU R epidemiological analysis
R-cran-epibasix
GNU R Elementary Epidemiological Functions
R-cran-epicalc
GNU R Epidemiological calculator
R-cran-epiestim
GNU R estimate time varying reproduction numbers from rpidemic curves
R-cran-epir
GNU R Functions for analysing epidemiological data
R-cran-epitools
GNU R Epidemiology Tools for Data and Graphics
R-cran-incidence
GNU R compute, handle, plot and model incidence of dated events
R-cran-lexrankr
extractive summarization of text with the LexRank algorithm
R-cran-seroincidence
GNU R seroincidence calculator tool
R-cran-sf
Simple Features for R
R-cran-sjplot
GNU R data visualization for statistics in social science
R-cran-surveillance
GNU R package for the Modeling and Monitoring of Epidemic Phenomena

Official Debian packages with lower relevance

Python3-epimodels
simple interface to simulate mathematical epidemic models in Python3
R-cran-cmprsk
GNU R subdistribution analysis of competing risks
R-cran-msm
GNU R Multi-state Markov and hidden Markov models in continuous time

Packaging has started and developers might try the packaging code in VCS

Chime
COVID-19 Hospital Impact Model for Epidemics
Epifire
model the spread of an infectious disease in a population
Netepi-analysis
network-enabled tools for epidemiology and public health practice
Netepi-collection
network-enabled tools for epidemiology and public health practice
R-cran-covid19
GNU R Coronavirus COVID-19 data acquisition and visualization
Shiny-server
put Shiny web apps online
Ushahidi
web platform for information collection

No known packages available but some record of interest (WNPP bug)

Repast
framework for creating agent based simulations

Hospital information systems - Debian Med suggestions for Hospital Information Systems

This metapackage contains dependencies for software and that could be useful ro run a Hospital Information System. While there is continuous work going on to package a ready to install system currently only preconditions are finished but hopefully helpful in hospitals anyway.

Official Debian packages with high relevance

Fis-gtm
metapackage for the latest version of FIS-GT.M database
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Care2x
integrated hospital information system
Openmrs
enterprise electronic medical record system framework
Tryton-modules-health
Tryton Application Platform (Health Module)
Vista-foia
metapackage for the latest version of vista-foia.

Unofficial packages built by somebody else

Oscar-mcmaster
Oscar (Web) A medical web application for electronic medical records

No known packages available but some record of interest (WNPP bug)

World-vista
repackage and extended version of VistA produced by WorldVistA

No known packages available

Hkma-cms
clinic management system
Ipath
telemedicine platform
Openeyes
ophthalmology electronic patient record system
Openmaxims
patient administration system and electronic patient record
Patientos
Healthcare Information System (HIS) for small hospitals and clinics

Imaging - Debian Med image processing and visualization packages

This metapackage will install Debian packages which might be useful in medical image processing and visualization.

On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows.

Official Debian packages with high relevance

Aeskulap
medical image viewer and DICOM network client
Amide
software for Medical Imaging
Ants
advanced normalization tools for brain and image analysis
Bart
tools for computational magnetic resonance imaging
Bart-view
viewer for multi-dimensional complex-valued data
Biosig-tools
format conversion tools for biomedical data formats
Camitk-imp
workbench application for the CamiTK library
Caret
Computerized Anatomical Reconstruction and Editing Toolkit
Conquest-common
ConQuest DICOM Server - common files
Ctn
Central Test Node, a DICOM implementation for medical imaging
Ctsim
Computed tomography simulator
Dcm2niix
next generation DICOM to NIfTI converter
Dcmtk
OFFIS DICOM toolkit command line utilities
Dicom3tools
DICOM medical image files manipulation and conversion tools
Dicomnifti
converts DICOM files into the NIfTI format
Dicomscope
OFFIS DICOM Viewer
Fslview
viewer for (f)MRI and DTI data
Gdf-tools
IO library for the GDF -- helper tools
Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
Gwyddion
Scanning Probe Microscopy visualization and analysis tool
Imagej
Image processing program with a focus on microscopy images
Imagevis3d
desktop volume rendering application for large data
Invesalius
3D medical imaging reconstruction software
Ismrmrd-tools
command-line tools for ISMRMRD
Itksnap
semi-automatic segmentation of structures in 3D images
King
interactive system for three-dimensional vector graphics
Libgdcm-tools
Grassroots DICOM tools and utilities
Lipsia
analysis suite for MRI and fMRI data
Medcon
Medical Image (DICOM, ECAT, ...) conversion tool
Mia-tools
Command line tools for gray scale image processing
Mia-viewit
Viewer program for 3D data sets created by using MIA
Mialmpick
Tools for landmark picking in 3D volume data sets
Minc-tools
MNI medical image format tools
Mriconvert
medical image file conversion utility
Mricron
magnetic resonance image conversion, viewing and analysis
Mrtrix3
diffusion-weighted MRI white matter tractography
Nifti-bin
tools shipped with the NIfTI library
Nifti2dicom
convert 3D medical images to DICOM 2D series
Odil
C++11 library for the DICOM standard (application)
Odin
develop, simulate and run magnetic resonance sequences
Openmeeg-tools
openmeeg library -- command line tools
Openslide-tools
Manipulation and conversion tools for OpenSlide
Orthanc
Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Pixelmed-apps
DICOM implementation containing Image Viewer and a ECG Viewer - cli
Plastimatch
medical image reconstruction and registration
Python3-dipy
Python library for the analysis of diffusion MRI datasets
Python3-nibabel
Python3 bindings to various neuroimaging data formats
Python3-nipy
Analysis of structural and functional neuroimaging data
Python3-nipype
Neuroimaging data analysis pipelines in Python3
Python3-nitime
timeseries analysis for neuroscience data (nitime)
Python3-pydicom
DICOM medical file reading and writing (Python 3)
Python3-pyxid
interface for Cedrus XID and StimTracker devices
Python3-surfer
visualize Freesurfer's data in Python3
Qnifti2dicom
convert 3D medical images to DICOM 2D series (gui)
Sigviewer
GUI viewer for biosignals such as EEG, EMG, and ECG
Slicer
software package for visualization and image analysis - main application
Sofa-apps
GUI for the Simulation Open Framework Architecture (SOFA)
Teem-apps
Tools to process and visualize scientific data and images - command line tools
Tifffile
Read and write image data from and to TIFF files
Via-bin
tools for volumetric image analysis
Voxbo
processing, statistical analysis, and display of brain imaging data
Vrrender
DICOM viewer
Vtk-dicom-tools
DICOM for VTK - tools
Xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)

Official Debian packages with lower relevance

Cmtk
Computational Morphometry Toolkit
Connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
Conquest-dbase
ConQuest DICOM Server - DBaseIII backend
Conquest-mysql
ConQuest DICOM Server - MySQL backend
Conquest-postgres
ConQuest DICOM Server - PostgreSQL backend
Conquest-sqlite
ConQuest DICOM Server - SQLite backend
Elastix
toolbox for rigid and nonrigid registration of images
Imagemagick
image manipulation programs -- binaries
Imview
Image viewing and analysis application
Openwalnut-qt4
Multi-modal medical and brain data visualization tool.
Orthanc-dicomweb
Plugin to extend Orthanc with support of WADO and DICOMweb
Orthanc-gdcm
DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
Orthanc-imagej
ImageJ plugin to import images from Orthanc
Orthanc-mysql
Plugins to use MySQL or MariaDB as a database back-end to Orthanc
Orthanc-postgresql
Plugins to use PostgreSQL as a database back-end to Orthanc
Orthanc-webviewer
Web viewer of medical images for Orthanc
Paraview
Parallel Visualization Application
Pngquant
PNG (Portable Network Graphics) image optimising utility
Science-workflow
workflow management systems useful for scientific research
Trimage
GUI and command-line interface to optimize image files

Debian packages in contrib or non-free

Bart-cuda
tools for computational magnetic resonance imaging
Fsl
transitional dummy package
Vmtk
the Vascular Modeling Toolkit

Packaging has started and developers might try the packaging code in VCS

Bioimagesuite
integrated image analysis software suite
Bioimagexd
Analyzing, processing and visualizing of multi dimensional microscopy images
Cellprofiler
quantitatively measure phenotypes from images automatically
Crea
base library of the creaTools medical image processing suite
Dicoogle
Java Advanced Imaging API reference implementation
Freesurfer
analysis and visualization of functional brain imaging data
Incf-nidash-oneclick-clients
utility for pushing DICOM data to the INCF datasharing server
Insightapplications
InsightToolKit (ITK) based medical imaging applications
Jist
Java Image Science Toolkit
Kradview
medical image viewer for DICOM images
Libdcm4che-java
Clinical Image and Object Management
Mayam
Cross-platform DICOM Viewer
Micromanager
Microscopy Software
Mipav
quantitative analysis and visualization of medical images
Mni-colin27-nifti
Talairach stereotaxic space template
Openelectrophy
data analysis GUI for intra- and extra-cellular recordings
Stabilitycalc
evaluate fMRI scanner stability
Visit
interactive parallel visualization and graphical analysis tool
Xnat
platform for data management and productivity tasks in neuroimaging

Unofficial packages built by somebody else

Cdmedicpacs
web interface to PACS to access DICOM study images
Fiji
The Fiji image processing suite (based on ImageJ)
Mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
Mni-n3
MNI Non-parametric Non-uniformity Normalization
Opendicom.net
API to DICOM in C# for Mono

No known packages available but some record of interest (WNPP bug)

Devide
Delft Visualization and Image processing Development Environment
Dtitk
DTI spatial normalization and atlas construction toolkit
Eeglab
toolbox for processing and visualization of electrophysiological data
Isis
I/O framework for neuroimaging data
Jemris
high performance computing MRI simulator
Opensourcepacs
medical image referral, archiving, routing and viewing system

No known packages available

Blox
medical imaging and visualization program
Brainvisa
image processing factory for MR images
Dcm4chee
Clinical Image and Object Management (enterprise)
Dicom4j
Java framework for Dicom
Drjekyll
interactive voxel editor for viewing and editing three-dimensional images
Dti-query
dynamic queries of the white matter brain pathways
Ecg2png
convert scanned electrocardiograms into PNG format
Gimias
Graphical Interface for Medical Image Analysis and Simulation
Hid
database management system for clinical imaging
Maris
package suite for Radiological Workflow
Medisnap
photograph, manage, view, compare, document and archive medical photos
Mesa-test-tools
IHE Test Software for Radiology
Miview
Medical Images viewer and converter
Mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
Mrisim
simulator for magnetic resonance imaging data
Omero
coming standard LIMS for microscopy images
Piano
medical image processing library for surgical planning
Pymeg
suite for analysis of magnetoencephalography (MEG) data
Stir
Software for Tomographic Image Reconstruction
Tempo
3D visualization of brain electrical activity

Imaging development - Debian Med image processing and visualization packages development

This metapackage will install Debian packages which might be useful for developing applications for medical image processing and visualization.

Official Debian packages with high relevance

Cimg-dev
powerful image processing library
Ctn-dev
Development files for Central Test Node, a DICOM implementation
Gmic
GREYC's Magic for Image Computing
Libbart-dev
Development files for BART
Libbiosig-dev
I/O library for biomedical data - development files
Libcamitk-dev
Computer Assisted Medical Intervention Tool Kit - development
Libcifti-dev
development files for CiftiLib
Libcv-dev
Translation package for libcv-dev
Libedf-dev
European Data Format library - devel
Libgdcm2-dev
Grassroots DICOM development libraries and headers
Libgdf-dev
IO library for the GDF -- development library
Libgiftiio-dev
IO library for the GIFTI cortical surface data format
Libinsighttoolkit4-dev
Image processing toolkit for registration and segmentation - development
Libismrmrd-dev
development files for ISMRMRD
Libmaxflow-dev
Development files for the maxflow-mincut algorithm
Libmdc2-dev
Medical Image (DICOM, ECAT, ...) conversion tool (development)
Libmia-2.4-dev
library for 2D and 3D gray scale image processing, development files
Libmialm-dev
Development files for the MIA landmark library
Libmiaviewit-dev
development files for the 3D visualization library
Libminc-dev
MNI medical image format development environment
Libnifti2-dev
IO libraries for the NIfTI-1 data format (development)
Libodil-dev
C++11 library for the DICOM standard (development files)
Libopenigtlink-dev
Open IGT Link is a simple network protocol - development
Libopenmeeg-dev
openmeeg library -- development files
Libopenslide-dev
Development files for the OpenSlide library
Libopensurgsim-dev
Free platform for surgical simulation - development
Libpapyrus3-dev
DICOM compatible file format library
Libsight-dev
Sight header files
Libsimpleitk1-dev
development files for SimpleITK
Libteem-dev
Tools to process and visualize scientific data and images - development
Libvia-dev
library for volumetric image analysis
Libvigraimpex-dev
development files for the C++ computer vision library
Libvistaio-dev
Development files for the libvistaio library
Libvolpack1-dev
fast volume rendering library (development package)
Libvtk-dicom-dev
DICOM for VTK - dev
Libvtk7-dev
VTK header files
Libxdf-dev
C++ library for loading XDF files (headers and static lib)
Octave-bart
Octave bindings for BART
Octave-dicom
manipulate DICOM files in Octave
Octave-gdf
IO library for the GDF -- Octave interface
Odin
develop, simulate and run magnetic resonance sequences
Python3-biosig
Python3 bindings for BioSig library
Python3-brian
simulator for spiking neural networks
Python3-dipy
Python library for the analysis of diffusion MRI datasets
Python3-gdcm
Grassroots DICOM Python bindings
Python3-imageio
library for reading and writing image data (Python 3)
Python3-mia
Python-3 bindings for the MIA image processing library
Python3-mne
Python modules for MEG and EEG data analysis
Python3-nibabel
Python3 bindings to various neuroimaging data formats
Python3-nipy
Analysis of structural and functional neuroimaging data
Python3-nipype
Neuroimaging data analysis pipelines in Python3
Python3-nitime
timeseries analysis for neuroscience data (nitime)
Python3-openslide
Python 3 wrapper for reading whole slide image files
Python3-pydicom
DICOM medical file reading and writing (Python 3)
Python3-pyxnat
Interface to access neuroimaging data on XNAT servers
Python3-simpleitk
Python bindings for SimpleITK
Python3-vigra
Python3 bindings for the C++ computer vision library
R-cran-rniftilib
GNU/R interface to NIFTICLIB

Official Debian packages with lower relevance

Libcamp-dev
C++ multi-purpose reflection library (development files)
Libeegdev-dev
Biosignal acquisition device library (Development files)
Libfreeimage-dev
Support library for graphics image formats (development files)
Libics-dev
Image Cytometry Standard file reading and writing (devel)
Liblimereg-dev
Library for lightweight image registration [development files]
Libnifti-doc
NIfTI library API documentation
Libvtk6-dev
VTK header files
Libxdffileio-dev
Library to read/write EEG data file formats (development files)
Tifffile
Read and write image data from and to TIFF files

Debian packages in contrib or non-free

Libvmtk-dev
shared links and header files for vmtk
Python-vmtk
Python interface for vmtk

Packaging has started and developers might try the packaging code in VCS

Emokit
Emotiv EPOC headset Python interface
Libbio-formats-java
reading and writing proprietary microscopy image data and metadata
Libctk-dev
toolkit for medical imaging application development - devel
Libopenslide-java
java wrapper for reading whole slide image files

Unofficial packages built by somebody else

Libmni-perllib-perl
The MNI Perl Library

Laboratory - Debian Med suggestions for medical laboratories

This metapackage contains dependencies for software and that could be useful ro run a medical laboratory.

Official Debian packages with high relevance

Opencfu
count cell colonies (CFUs) on agar plates by processing digital pictures
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Openfreezer
Laboratory analysis, research and investigation software application

No known packages available

Catissuesuite
tool for biospecimen inventory management
Openelis
Enterprise Laboratory Information System

Oncology - Debian Med packages for oncology

This metapackage will install tools that are useful for radiation oncology.

Official Debian packages with high relevance

Dicompyler
radiation therapy research platform
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Simrisc
simulation model for breast cancer risk

Official Debian packages with lower relevance

Python3-dicompylercore
core radiation therapy modules for DICOM / DICOM RT used by dicompyler

Packaging has started and developers might try the packaging code in VCS

Uw-prism
software tools for radiation therapy planning

No known packages available

Planunc
tools for radiotherapy treatment planning

Pharmacology - Debian Med packages for pharmaceutical research

This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research.

Official Debian packages with high relevance

Chemtool
chemical structures drawing program
R-cran-dosefinding
Planning and Analyzing Dose Finding experiments
R-cran-rpact
Confirmatory Adaptive Clinical Trial Design and Analysis

Debian packages in contrib or non-free

Raccoon
preparation of in silico drug screening projects

Physics - Debian Med packages for medical physicists

This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields.

Official Debian packages with high relevance

Biosig-tools
format conversion tools for biomedical data formats
Gdf-tools
IO library for the GDF -- helper tools
Octave
GNU Octave language for numerical computations
Paw
Physics Analysis Workstation - a graphical analysis program
Paw++
Physics Analysis Workstation (Lesstif-enhanced version)
R-base
GNU R statistical computation and graphics system

Official Debian packages with lower relevance

Libbiosig-dev
I/O library for biomedical data - development files
Octave-biosig
Octave bindings for BioSig library
Paw-demos
Physics Analysis Workstation examples and tests
Python3-biosig
Python3 bindings for BioSig library
Python3-multipletau
multiple-tau algorithm for Python3/NumPy

No known packages available but some record of interest (WNPP bug)

Gate
Geant4 Application for Emission Tomography
Openvibe
platform for the design, test and use of BCI

Practice - Debian Med packages for practice management

This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice.

Official Debian packages with high relevance

Entangle
Tethered Camera Control & Capture
Freediams
pharmaceutical drug prescription and interaction manager
Freemedforms-emr
electronic medical record manager
Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
Gnumed-client
medical practice management - Client
Gnumed-server
medical practice management - server
Libchipcard-tools
tools for accessing chipcards
Orthanc
Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
Oscar
Open Source CPAP Analysis Reporter (OSCAR)
Qrisk2
cardiovascular disease risk calculator
R-cran-medadherence
GNU R Medication Adherence: Commonly Used Definitions

Official Debian packages with lower relevance

Libctapimkt1
Read German Krankenversichertenkarte and eGK

Packaging has started and developers might try the packaging code in VCS

Freeshim
opensource electronic medical device interface
Openemr
Comprehensive medical practice management
Thera-pi
organization and management of outpatient clinics and rehabilitation-medicine companies

Unofficial packages built by somebody else

Elementalclinic
Electronical Medical Health record system for mental health
Freemed
Electronic Medical Record and Practice Management system
Tinyheb
billing system for midwives

No known packages available but some record of interest (WNPP bug)

Elexis
medical practice managemant system for use in Switzerland
Openrep
software for homeopathic repertorization and viewing materia medicae

No known packages available

Clearhealth
Medical practice management system
Freeb
Medical Bill formating module
Medintux
Medical practice management system
Mirrormed
EHR and practice management system
Mirth
HL7 integration engine
Openpms
medical billing, scheduling, and account management system
Proteus
clinical decision support guidelines model
Remitt
preparing and submitting medical billing data
Resmedicinae
comprising software solution for use in medicine
Sqlclinic
intranet solution for Saint Vincents Catholic Medical Centers of New York

Psychology - Debian Med packages for psychology

This metapackage contains dependencies for a collection of software which might be helpful for psychological research.

Official Debian packages with high relevance

Praat
program for speech analysis and synthesis
Psignifit
Fitting and testing hypotheses about psychometric functions
Psychopy
environment for creating psychology stimuli in Python
R-cran-foreign
GNU R package to read/write data from other stat. systems
R-cran-psy
GNU R procedures for psychometrics
R-cran-psych
GNU R procedures for psychological, psychometric, and personality research
R-cran-psychometric
GNU R applied psychometric theory
R-cran-psychotree
GNU R recursive partitioning based on psychometric models
R-cran-psyphy
functions for analyzing psychophysical data in GNU R

Official Debian packages with lower relevance

Python-pyepl
module for coding psychology experiments in Python
Python3-bids-validator
validator for the Brain Imaging Data Structure (BIDS) datasets
Python3-bmtk
development package for building, simulating and analysing large-scale networks
Science-psychophysics
Debian Science packages for Psychophysics

Rehabilitation - Debian Med packages for rehabilitation technologies

This metapackage will install tools that are useful for rehabilitation and therapy.

Official Debian packages with high relevance

Sitplus
Free software framework for ludic-therapeutic activities

Official Debian packages with lower relevance

Aghermann
Sleep-research experiment manager

Research - Debian Med packages for medical research

This metapackage will install tools that are useful for medical research.

Official Debian packages with high relevance

R-cran-rpact
Confirmatory Adaptive Clinical Trial Design and Analysis

No known packages available but some record of interest (WNPP bug)

Openclinica
electronic data capture and clinical data management

Statistics - Debian Med statistics

This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care.

Official Debian packages with high relevance

R-bioc-edger
Empirical analysis of digital gene expression data in R
R-bioc-limma
linear models for microarray data
R-bioc-multtest
Bioconductor resampling-based multiple hypothesis testing
R-bioc-qvalue
GNU R package for Q-value estimation for FDR control
R-cran-ade4
GNU R analysis of ecological data
R-cran-beeswarm
bee swarm plot, an alternative to stripchart
R-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-randomforest
GNU R package implementing the random forest classificator
R-cran-rwave
GNU R time-frequency analysis of 1-D signals
R-cran-snowfall
GNU R easier cluster computing (based on snow)
R-cran-waveslim
GNU R wavelet routines for 1-, 2- and 3-D signal processing
R-cran-wavethresh
GNU R wavelets statistics and transforms

Official Debian packages with lower relevance

Science-statistics
Debian Science Statistics packages

Packaging has started and developers might try the packaging code in VCS

Rstudio
GNU R IDE

Tools - Debian Med several tools

This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health.

Official Debian packages with high relevance

Cronometer
CRON-o-Meter - Exercise and nutrient intake tracker
Edfbrowser
viewer for biosignal storage files such as bdf and edf
Galileo
Utility to securely synchronize a Fitbit device with the Fitbit web service
Hunspell-de-med
German medical dictionary for hunspell
Hunspell-en-med
English medical dictionary for hunspell
Nut-nutrition
dietary nutrition analysis software
Nutsqlite
Dietary nutrition analysis software
Pcalendar
track menstrual cycles and predict fertility periods
Pondus
personal weight manager for GTK+2
Python3-fitbit
FitBit REST API Client Implementation - Python 3
Quitcount
Small tool which may help yourself quit smoking
R-cran-fitbitscraper
Import your Fitbit data from the Fitbit's website into R
R-cran-fitcoach
R package for analysis and retrieve data of Fitbit
Wgerman-medical
German medical dictionary words for /usr/share/dict
Workrave
Repetitive Strain Injury prevention tool

Official Debian packages with lower relevance

Cycle
calendar program for women
Entangle
Tethered Camera Control & Capture
Goldencheetah
set of analysis tools for cycling performance
Mencal
menstruation calendar
Oscar
Open Source CPAP Analysis Reporter (OSCAR)

Debian packages in contrib or non-free

Mssstest
Normalisation of disease scores for patients with Multiple Sclerosis

Packaging has started and developers might try the packaging code in VCS

Pesco
Cognitive stimulation tool for elderly or cognitively impaired

Typesetting - Debian Med support for typesetting and publishing

This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology.

Official Debian packages with high relevance

King
interactive system for three-dimensional vector graphics
Texlive-latex-extra
TeX Live: LaTeX additional packages
Texlive-science
TeX Live: Mathematics, natural sciences, computer science packages

Official Debian packages with lower relevance

Biber
Much-augmented BibTeX replacement for BibLaTeX users
Bibus
bibliographic database
Jabref-plugin-oo
LibreOffice plugin for JabRef (transitional dummy package)
Kbibtex
BibTeX editor for KDE
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots