Tasks page

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

Table of contents

• Biology
• Biology development
• Next generation sequencing
• Phylogeny
• Cloud
• Content management
• Medical data
• Dental
• Epidemiology
• Hospital information systems
• Imaging
• Imaging development
• Laboratory
• Oncology
• Pharmacology
• Physics
• Practice
• Psychology
• Rehabilitation
• Research
• Statistics
• Tools
• Typesetting

Biology - pacotes Debian Med para micro-biologia

Este meta pacote instalará os pacotes Debian relacionados com biologia molecular, biologia estrutural e bioinformática para uso nas ciências da vida.

Official Debian packages with high relevance

Abacas

contiguação automática baseada em algoritmo de sequências montadas

Acedb-other

recuperação de DNA ou sequências de proteínas

Acedb-other-belvu

editor de alinhamento de sequência múltipla

Acedb-other-dotter

visualisation of sequence similarity

Adun-core

Molecular Simulator

Aegean

integrated genome analysis toolkit

Aevol

digital genetics model to run Evolution Experiments in silico

Alien-hunter

Temas de Ordem Variável Interpolados para identificar DNA adquirido horizontalmente

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

Artemis

genome browser and annotation tool

Artfastqgenerator

ouputs artificial FASTQ files derived from a reference genome

Autodock

análise das ligações do ligante à estrutura de proteína

Autodock-vina

docking of small molecules to proteins

Autogrid

pré-calcula ligações de ligantes aos seus receptores

Axe-demultiplexer

Trie-based DNA sequencing read demultiplexer

Ballview

ferramenta livre de modelagem e gráficos moleculares

Bamtools

toolkit for manipulating BAM (genome alignment) files

Barrnap

rapid ribosomal RNA prediction

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

Biomaj

biological data-bank updater

Blasr

mapping single-molecule sequencing reads

Blast2

Basic Local Alignment Search Tool ("Fer. Básica de Busca de Alinhamento Local")

Bowtie

Ultrafast memory-efficient short read aligner

Bowtie2

ultrafast memory-efficient short read aligner

Boxshade

embelezador de impressão de alinhamentos de seqüência múltipla

Brig

BLAST Ring Image Generator

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

Cgview

Circular Genome Viewer

Chimeraslayer

detects likely chimeras in PCR amplified DNA

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

Clustalx

Multiple alignment of nucleic acid and protein sequences (graphical interface)

Codonw

Correspondence Analysis of Codon Usage

Concavity

predictor of protein ligand binding sites from structure and conservation

Conservation-code

protein sequence conservation scoring tool

Daligner

local alignment discovery between long nucleotide sequencing reads

Dawg

program to simulate the evolution of recombinant DNA sequences

Dazzdb

manage nucleotide sequencing read data

Dialign

Segment-based multiple sequence alignment

Dialign-tx

alinhador de seqüências múltiplas baseado em segmentos

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

Dwgsim

short sequencing read simulator

Ea-utils

command-line tools for processing biological sequencing data

Ecopcr

estimate PCR barcode primers quality

Edtsurf

triangulated mesh surfaces for protein structures

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

Falconkit

genome assembly toolkit

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

Fastqc

quality control for high throughput sequence data

Fasttree

phylogenetic trees from alignments of nucleotide or protein sequences

Fastx-toolkit

FASTQ/A short nucleotide reads pre-processing tools

Ffindex

simple index/database for huge amounts of small files

Figtree

graphical phylogenetic tree viewer

Filo

FILe and stream Operations

Fitgcp

fitting genome coverage distributions with mixture models

Flexbar

flexible barcode and adapter removal for sequencing platforms

Freecontact

fast protein contact predictor

Gamgi

General Atomistic Modelling Graphic Interface (GAMGI)

Garlic

um programa de visualização para biomoléculas

Gasic

genome abundance similarity correction

Gbrowse

GMOD Generic Genome Browser

Gdpc

visualizador de simulações moleculares dinâmicas

Genometools

versatile genome analysis toolkit

Gentle

suite to plan genetic cloning

Gff2aplot

pair-wise alignment-plots for genomic sequences in PostScript

Gff2ps

produz saída PostScript gráfica a partir de arquivos GFF

Ghemical

Ambiente de modelagem molecular GNOME

Giira

RNA-Seq driven gene finding incorporating ambiguous reads

Glam2

gapped protein motifs from unaligned sequences

Grinder

Versatile omics shotgun and amplicon sequencing read simulator

Gromacs

simulador de dinâmica molecular, com ferramentas de construção e análise

Gubbins

phylogenetic analysis of genome sequences

Gwama

Genome-Wide Association Meta Analysis

Hhsuite

sensitive protein sequence searching based on HMM-HMM alignment

Hmmer

perfis "hidden Markov models" para análise de seqüência de proteína

Hmmer2

perfis "hidden Markov models" para análise de seqüência de proteína

Hyphy-mpi

Hypothesis testing using Phylogenies (MPI version)

Hyphy-pt

Hypothesis testing using Phylogenies (pthreads version)

Hyphygui

Hypothesis testing using Phylogenies (GTK+ gui)

Idba

iterative De Bruijn Graph De Novo short read assembler for transcriptome

Indelible

powerful and flexible simulator of biological evolution

Infernal

inference of RNA secondary structural alignments

Ipig

integrating PSMs into genome browser visualisations

Iqtree

efficient phylogenetic software by maximum likelihood

Jaligner

Smith-Waterman algorithm with Gotoh's improvement

Jalview

multiple alignment editor

Jellyfish

count k-mers in DNA sequences

Jmol

visualizador molecular

Kalign

Global and progressive multiple sequence alignment

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

Kmc

count kmers in genomic sequences

Kmer

suite of tools for DNA sequence analysis

Kraken

assigning taxonomic labels to short DNA sequences

Last-align

genome-scale comparison of biological sequences

Leaff

biological sequence library utilities and applications

Librg-utils-perl

parsers and format conversion utilities used by (e.g.) profphd

Logol-bin

Pattern matching tool using Logol language

Loki

MCMC linkage analysis on general pedigrees

Ltrsift

postprocessing and classification of LTR retrotransposons

Macs

Model-based Analysis of ChIP-Seq on short reads sequencers

Macsyfinder

Detection of macromolecular systems in protein datasets.

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

Maqview

graphical read alignment viewer for short gene sequences

Massxpert

linear polymer mass spectrometry software

Mauve-aligner

multiple genome alignment

Melting

compute the melting temperature of nucleic acid duplex

Meryl

in- and out-of-core kmer counting and utilities

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

Minia

short-read biological sequence assembler

Miniasm

ultrafast de novo assembler for long noisy DNA sequencing reads

Minimap

tool for approximate mapping of long biosequences such as DNA reads

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

alinhamento eficiente de seqüência para genomas completos

Murasaki

homology detection tool across multiple large genomes

Muscle

programa de alinhamento múltiplo de sequências de proteína

Mustang

multiple structural alignment of proteins

Nanopolish

consensus caller for nanopore sequencing data

Nast-ier

NAST-based DNA alignment tool

Ncbi-blast+

next generation suite of BLAST sequence search tools

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

bibliotecas NCBI para aplicações de biologia (utilitários baseados em X)

Ncl-tools

tools to deal with NEXUS files

Ncoils

coiled coil secondary structure prediction

Neobio

computes alignments of amino acid and nucleotide sequences

Njplot

phylogenetic tree drawing program

Norsnet

tool to identify unstructured loops in proteins

Norsp

predictor of non-regular secondary structure

Openms

package for LC/MS data management and analysis

Paraclu

Parametric clustering of genomic and transcriptomic features

Parsinsert

Parsimonious Insertion of unclassified sequences into phylogenetic trees

Pbalign

map Pacific Biosciences reads to reference DNA sequences

Pbbarcode

annotate PacBio sequencing reads with barcode information

Pbdagcon

sequence consensus using directed acyclic graphs

Pbgenomicconsensus

Pacific Biosciences variant and consensus caller

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

Desenho gráfico de iniciadores para PCR

Perm

efficient mapping of short reads with periodic spaced seeds

Phybin

binning/clustering newick trees by topology

Phylip

package of programs for inferring phylogenies

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

Piler

genomic repeat analysis

Placnet

Plasmid Constellation Network project

Plasmidomics

desenha plasmídeos e mapas vetoriais com exportação de gráficos em PostScript

Plast

Parallel Local Sequence Alignment Search Tool

Plink

whole-genome association analysis toolset

Plink1.9

whole-genome association analysis toolset

Poa

Partial Order Alignment for multiple sequence alignment

Populations

population genetic software

Poretools

toolkit for nanopore nucleotide sequencing data

Prank

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

Predictnls

prediction and analysis of protein nuclear localization signals

Predictprotein

suite of protein sequence analysis tools

Prime-phylo

bayesian estimation of gene trees taking the species tree into account

Primer3

ferramenta para desenhar acompanhamento de oligo nucleotídeos para amplificação de DNA

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

alinhamento múltiplo de seqüências de proteína

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

Proteinortho

Detection of (Co-)orthologs in large-scale protein analysis

Prottest

selection of best-fit models of protein evolution

Pycorrfit

tool for fitting correlation curves on a logarithmic plot

Pymol

sistema de gráficos de moléculas

Pynast

alignment of short DNA sequences

Pyscanfcs

scientific tool for perpendicular line scanning FCS

Python-cogent

framework for genomic biology

Qiime

Quantitative Insights Into Microbial Ecology

R-bioc-annotate

BioConductor annotation for microarrays

R-bioc-biostrings

GNU R string objects representing biological sequences

R-bioc-cummerbund

tool for analysis of Cufflinks RNA-Seq output

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-gviz

Plotting data and annotation information along genomic coordinates

R-bioc-hilbertvis

GNU R package to visualise long vector data

R-bioc-limma

linear models for microarray data

R-bioc-rtracklayer

GNU R interface to genome browsers and their annotation tracks

R-cran-ape

GNU R package for Analyses of Phylogenetics and Evolution

R-cran-bio3d

GNU R package for biological structure analysis

R-cran-genabel

GNU R package for genome-wide SNP association analysis

R-cran-phangorn

GNU R package for phylogenetic analysis

R-cran-qtl

GNU R package for genetic marker linkage analysis

R-cran-seqinr

GNU R biological sequences retrieval and analysis

R-cran-vegan

Community Ecology Package for R

R-other-mott-happy.hbrem

GNU R package for fine-mapping complex diseases

Rasmol

visualize macromoléculas biológicas

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

Reapr

universal tool for genome assembly evaluation

Relion-bin

toolkit for 3D reconstructions in cryo-electron microscopy

Relion-bin+gui

parallel toolkit for 3D reconstructions in cryo-electron microscopy

Relion-bin+mpi

parallel toolkit for 3D reconstructions in cryo-electron microscopy

Relion-bin+mpi+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

Rna-star

ultrafast universal RNA-seq aligner

Rnahybrid

Fast and effective prediction of microRNA/target duplexes

Roary

high speed stand alone pan genome pipeline

Rsem

RNA-Seq by Expectation-Maximization

Rtax

Classification of sequence reads of 16S ribosomal RNA gene

Saint

Significance Analysis of INTeractome

Salmon

wicked-fast transcript quantification from RNA-seq data

Samtools

processing sequence alignments in SAM and BAM formats

Scrm

simulator of evolution of genetic sequences

Scythe

Bayesian adaptor trimmer for sequencing reads

Seaview

Multiplatform interface for sequence alignment and phylogeny

Seqan-apps

C++ library for the analysis of biological sequences

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

Sibsim4

seqüências de RNA expressadas em alinhamento em um modelo de DNA

Sickle

windowed adaptive trimming tool for FASTQ files using quality

Sigma-align

Simple greedy multiple alignment of non-coding DNA sequences

Sim4

ferramenta para alinhamento cDNA e DNA genômico

Sim4db

batch spliced alignment of cDNA sequences to a target genome

Smalt

Sequence Mapping and Alignment Tool

Snap

location of genes from DNA sequence with hidden markov model

Snap-aligner

Scalable Nucleotide Alignment Program

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

Spread-phy

analyze and visualize phylogeographic reconstructions

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

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 maniuplating DNA sequencing files

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

Swarm

robust and fast clustering method for amplicon-based studies

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

Tigr-glimmer

Gene detection in archea and bacteria

Tm-align

structual alignment of proteins

Tophat

fast splice junction mapper for RNA-Seq reads

Topp

set of programs implementing The OpenMS Proteomic Pipeline

Toppred

transmembrane topology prediction

Transdecoder

find coding regions within RNA transcript sequences

Transrate-tools

helper for transrate

Transtermhp

find rho-independent transcription terminators in bacterial genomes

Tree-ppuzzle

reconstrução paralelizada de árvores filogenéticas por máxima probabilidade

Tree-puzzle

reconstrução de árvores filogenéticas por máxima probabilidade

Treeview

Java re-implementation of Michael Eisen's TreeView

Treeviewx

Displays and prints phylogenetic trees

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

Varna

Visualization Applet for RNA

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

Wigeon

reimplementation of the Pintail 16S DNA anomaly detection utility

Wise

comparison of biopolymers, like DNA and protein sequences

Zalign

parallel local alignment of biological sequences

Official Debian packages with lower relevance

Adun.app

Molecular Simulator for GNUstep (GUI)

Cain

simulations of chemical reactions

Emboss-explorer

web-based GUI to EMBOSS

Maude

high-performance logical framework

Melting-gui

interface gráfica para calcular a temperatura de fusão do duplex de ácido nucleico

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

Mobyle

Web portal that provides web forms for command-line software

Mobyle-programs

Program descriptions for the mobyle portal

Mobyle-tutorials

program tutorials for the mobyle portal

Mrs

Information Retrieval System for Biomedical databanks

R-bioc-aroma.light

BioConductor methods normalization and visualization of microarray data

R-cran-boolnet

assembling, analyzing and visualizing Boolean networks

Debian packages in contrib or non-free

Abyss

de novo, parallel, sequence assembler for short reads

Arb

phylogenetic sequence analysis suite - main program

Autodocktools

GUI to help set up, launch and analyze AutoDock dockings

Beast-mcmc

Bayesian MCMC phylogenetic inference

Biomaj-watcher

biological data-bank updater - web interface

Blimps-utils

blocks database improved searcher

Cluster3

Reimplementation of the Eisen-clustering software

Cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq

Eigensoft

reduction of population bias for genetic analyses

Embassy-phylip

EMBOSS conversions of the programs in the phylip package

Gmap

spliced and SNP-tolerant alignment for mRNA and short reads

Igv

Integrative Genomics Viewer

Paml

Phylogenetic Analysis by Maximum Likelihood (PAML)

Raccoon

preparation of in silico drug screening projects

Seq-gen

simulate the evolution of nucleotide or amino acid sequences

Sift

predicts if a substitution in a protein has a phenotypic effect

Ugene

integrated bioinformatics toolkit

Varscan

variant detection in next-generation sequencing data

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

Acacia

Error-corrector for pyrosequenced amplicon reads.

Amos-assembler

modular whole genome assembler

Apollo

genome annotation viewer and editor

Ariba

Antibiotic Resistance Identification By Assembly

Art-nextgen-simulation-tools

simulation tools to generate synthetic next-generation sequencing reads

Axparafit

optimized statistical analysis of host-parasite coevolution

Axpcoords

highly optimized and parallelized porting of pcoords

Bagpipe

genomewide LD mapping

Biceps

error-tolerant peptide identification

Bigsdb

Bacterial Isolate Genome Sequence Database

Bitseq

Bayesian Inference of Transcripts from Sequencing Data

Blat

BLAST-Like Alignment Tool

Cinema

multi-sequence alignment editor and viewer.

Circlator

circularize genome assemblies

Clonalorigin

inference of homologous recombination in bacteria using whole genome sequences

Condetri

straight-forward trimming of FASTQ sequences

Coot

model building program for macromolecular crystallography

Crac

integrated RNA-Seq read analysis

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

Dindel

determines indel calls from short-read data

Ecell

Concept and environment for constructing virtual cells on computers

Emmax

genetic mapping considering population structure

Emperor

tool for visualizing high-throughput microbial community data

Ensembl

basic Ensembl genome browser

Fasta3

tools for searching collections of biological sequences

Ffp

Feature Frequency Profile Phylogeny

Forester

Graphical vizualiation tool Archaeopteryx

Freebayes

Bayesian haplotype-based polymorphism discovery and genotyping

Fsa

Fast Statistical Alignment of protein, RNA or DNA sequences

Garli

phylogenetic analysis of molecular sequence data using maximum-likelihood

Gassst

Global alignment short sequence search tool

Gatk

The Genome Analysis Toolkit

Grabix

wee tool for random access into BGZF files

Grogui

graphical user interface for popular molecular dynamics package GROMACS

Haploview

Analysis and visualization of LD and haplotype maps

Harvest-tools

archiving and postprocessing for reference-compressed genomic multi-alignments

Hawkeye

Interactive Visual Analytics Tool for Genome Assemblies

Htqc

Quality control and filtration for illumina sequencing data

Inspect

mass-spectrometry database search tool

Iva

iterative virus assembler

Jbrowse

The JBrowse Genome Browser

Jmodeltest

HPC selection of models of nucleotide substitution

Kclust

clustering of protein sequences

Kempbasu

Significance tests for comparing digital gene expression profiles

Lagan

highly parametrizable pairwise global alignment program

Lofreq

sensitive variant calling from sequencing data

Logomat-m

visualize central aspects of Profile Hidden Markov Models (pHMMs)

Mach-haplotyper

Markov Chain based SNP haplotyper

Mage2tab

MAGE-MLv1 converter and visualiser

Martj

distributed data integration system for biological data

Meme

search for common motifs in DNA or protein sequences

Metastudent-data-3

predictor of Gene Ontology terms from protein sequence - data #3

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

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

Obitools

programs to analyze NGS data in a DNA metabarcoding context

Pal2nal

converts proteins to genomic DNA alignment

Partitionfinder

choses partitioning schemes and models of molecular evolution for sequence data

Patman

rapid alignment of short sequences to large databases

Patristic

Calculate patristic distances and comparing the components of genetic change

Pcma

fast and accurate multiple sequence alignment based on profile consistency

Phyloviz-core

phylogenetic inference and data visualization for sequence based typing methods

Pipasic

Protein Abundance Correction in Metaproteomic Data

Plato

Analysis, translation, and organization of large-scale genetic data

Plip

fully automated protein-ligand interaction profiler

Profit

Protein structure alignment

Prokka

rapid annotation of prokaryotic genomes

Pscan-tfbs

search for transcription factor binding sites

Psipred

protein secondary structure prediction

Pssh2

set of scripts for mapping protein sequence to structure

Python-reaper

QTL analysis for expression data

Qualimap

evaluating next generation sequencing alignment data

R-cran-metamix

GNU R bayesian mixture analysis for metagenomic community profiling

R-other-apmswapp

GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry

R-other-valdar-bagphenotype.library

GNU R extension of the functionality of happy

Rambo-k

Read Assignment Method Based On K-mers

Repeatmasker

screen DNA sequences for interspersed repeats

Roadtrips

case-control association testing with unknown population and pedigree structure

Rosetta

molecular biophysics for structural biology

Sap

Pairwise protein structure alignment via double dynamic programming

Sequenceconverter.app

biological sequence file format conversion applet for GNUstep

Situs

Modeling of atomic resolution structures into low-resolution density maps

Smrtanalysis

software suite for single molecule, real-time sequencing

Snpeff

annotation and effect prediction tool for genome sequences

Srst2

Short Read Sequence Typing for Bacterial Pathogens

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

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

Trnascan-se

detection of transfer RNA genes in genomic sequence

Unc-fish

Fast Identification of Segmental Homology

Vienna-rna

RNA sequence analysis

Vmd

presentation of traces of molecular dynamics runs

Wgs-assembler

Whole-Genome DNA sequence assembler

Zodiac-zeden

ZODIAC - Zeden's Organise DIsplay And Compute

Unofficial packages built by somebody else

Beads

2-DE electrophoresis gel image spot detection

Big-blast

Helper tool to run blast on large sequences

Blixem

interactive browser of pairwise Blast matches

Caftools

Tools to maintain DNA sequence assemblies

Cap3

DNA Sequence Assembly Program

Coalesce

outdated program to estimate population-genetic parameters

Compclust

explore and quantify relationships between clustering results

Estferret

processes, clusters and annotates EST data

Estscan

detect coding regions in DNA sequences, even if of low quality

Fasta

searching DNA and protein databases

Fluctuate

outdated program to model a single population

Lamarc

estimate population-genetic parameters

Lucy

DNA sequence quality and vector trimming tool

Maxd

data warehouse and visualisation environment for genomic expression data

Mesquite

help biologists analyze comparative data about organisms

Migrate

estimation of population sizes and gene flow using the coalescent

Modeller

MODELLER provides three dimensional structures of proteins by satisfaction

Msatfinder

identification and characterization of microsatellites in a comparative genomic context

Mview

reformat results of a sequence database search or a multiple alignment

Oligoarrayaux

Prediction of Melting Profiles for Nucleic Acids

Omegamap

detecting natural selection and recombination in DNA or RNA sequences

Partigene

generating partial gemomes

Pfaat

Protein Family Alignment Annotation Tool

Pftools

tools to handle profiles of protein domains from PROSITE

Prot4est

EST protein translation suite

Python-orange

Data mining framework

Qtlcart

map quantitative traits using a map of molecular markers

Rbs-finder

find ribosome binding sites(RBS)

Recombine

effective population size of populations

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

Trace2dbest

process trace files into dbEST submissions

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

Btk-core

biomolecule Toolkit C++ library

Galaxy

manipulate sequences and annotation files

Mirbase

The microRNA sequence database

Phylowin

Graphical interface for molecular phylogenetic inference

No known packages available

Amoscmp

comparative genome assembly package

Arachne

toolkit for Whole Genome Shotgun Assembly

Asap

organize the data associated with a genome

Augustus

predict genes in eukaryotic genomic sequences

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

Das-proserver

lightweight Distributed Annotation System (DAS) server

Decipher

tracks duplications and deletions of DNA in patients

E-hive

distributed processing system based on 'autonomous agents'

Elph

motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites

Est-db

Software suite for expressed sequence tag (EST) sequencing

Exalt

phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

Excavator

gene expression data clustering

Figaro

novel vector trimming software

Finex

sequence homology searching

Forge

genome assembler for mixed read types

Gbioseq

DNA sequence editor for Linux

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

Hexamer

scan DNA sequences to look for likely coding regions

Hilbertvisgui

interactive tool to visualize long vectors of integer data by means of Hilbert curves

Jigsaw

gene prediction using multiple sources of evidence

Jstreeview

Editor for Phylogenetic Trees

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

Rmblast

RepeatMasker compatible version of the standard NCBI BLAST

Rose

Region-Of-Synteny Extractor

Spice

Distributed Annotation System (DAS) client

Tigr-assembler

whole-genome assembly

Tracetuner

DNA sequencing and trace processing

Treebuilder3d

viewer of SAGE and other types of gene expression data

Treetime

Bayesian sampling of phylogenetic trees from molecular 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 micro-biology applications

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

Official Debian packages with high relevance

Bioperl

Ferramentas Perl para biologia molecular computacional

Bioperl-run

BioPerl wrappers: scripts

Biosquid

utilities for biological sequence analysis

Libai-fann-perl

Perl wrapper for the FANN library

Libbio-mage-perl

Container module for classes in the MAGE package: MAGE

Libbiojava-java

Java API to biological data and applications (default version)

Libbiojava3-java

Java API to biological data and applications (default version)

Libbiojava4-java

Java API to biological data and applications (default version)

Libfreecontact-perl

fast protein contact predictor - binding for Perl

Libfreecontact0-dev

fast protein contact predictor library - development files

Libgenome-1.3-dev

toolkit for developing bioinformatic related software (devel)

Libgo-perl

perl modules for GO and other OBO ontologies

Libhtsjdk-java

Java API for high-throughput sequencing data (HTS) formats

Libmems-1.6-dev

development library to support DNA string matching and comparative genomics

Libmuscle-3.7-dev

multiple alignment development library for protein sequences

Libncbi6-dev

NCBI libraries for biology applications (development files)

Libnhgri-blastall-perl

Perl extension for running and parsing NCBI's BLAST 2.x

Libtfbs-perl

scanning DNA sequence with a position weight matrix

Libvibrant6-dev

bibliotecas NCBI para aplicações gráficas de biologia (arquivos de desenvolvimento)

Mcl

Markov Cluster algorithm

Python-biopython

Python library for bioinformatics (implemented in Python 2)

Python-cogent

framework for genomic biology

Python-cutadapt

Clean biological sequences from high-throughput sequencing reads

Python-screed

short nucleotide read sequence utils in Python 2

Python3-biopython

Python library for bioinformatics (implemented in Python 3)

Python3-cutadapt

Clean biological sequences from high-throughput sequencing reads

R-cran-genetics

GNU R package for population genetics

R-cran-haplo.stats

GNU R package for haplotype analysis

Ruby-bio

Ruby tools for computational molecular biology

Official Debian packages with lower relevance

Libfreecontact-doc

documentation for libfreecontact

Python-biopython-doc

Documentation for the Biopython library

Python-biopython-sql

Biopython support for the BioSQL database schema (Python 2)

Python3-biopython-sql

Biopython support for the BioSQL database schema (Python 3)

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

It aims at gettting packages which specializes in alignment of sequences produced by next generation sequencing.

Official Debian packages with high relevance

Bedtools

suite of utilities for comparing genomic features

Bowtie

Ultrafast memory-efficient short read aligner

Bwa

Burrows-Wheeler Aligner

Fastx-toolkit

FASTQ/A short nucleotide reads pre-processing tools

Filo

FILe and stream Operations

Kissplice

Detection of various kinds of polymorphisms in RNA-seq data

Last-align

genome-scale comparison of biological sequences

Maq

maps short fixed-length polymorphic DNA sequence reads to reference sequences

Mira-assembler

Whole Genome Shotgun and EST Sequence Assembler

Mothur

sequence analysis suite for research on microbiota

Picard-tools

Command line tools to manipulate SAM and BAM files

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

Samtools

processing sequence alignments in SAM and BAM formats

Sra-toolkit

utilities for the NCBI Sequence Read Archive

Ssake

genomics application for assembling millions of very short DNA sequences

Tabix

generic indexer for TAB-delimited genome position files

Tophat

fast splice junction mapper for RNA-Seq reads

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

Debian packages in contrib or non-free

Cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq

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

Dindel

determines indel calls from short-read data

Mosaik-aligner

reference-guided aligner for next-generation sequencing

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

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

alinhador de seqüências múltiplas baseado em segmentos

Exonerate

generic tool for pairwise sequence comparison

Fastdnaml

Tool for construction of phylogenetic trees of DNA sequences

Figtree

graphical phylogenetic tree viewer

Hmmer

perfis "hidden Markov models" para análise de seqüência de proteína

Iqtree

efficient phylogenetic software by maximum likelihood

Kalign

Global and progressive multiple sequence alignment

Mrbayes

Bayesian Inference of Phylogeny

Muscle

programa de alinhamento múltiplo de sequências de proteína

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

Proalign

Probabilistic multiple alignment program

Probalign

multiple sequence alignment using partition function posterior probabilities

Probcons

PROBabilistic CONSistency-based multiple sequence alignment

Proda

alinhamento múltiplo de seqüências de proteína

Prottest

selection of best-fit models of protein evolution

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

structual alignment of proteins

Tree-ppuzzle

reconstrução paralelizada de árvores filogenéticas por máxima probabilidade

Tree-puzzle

reconstrução de árvores filogenéticas por máxima probabilidade

Treeview

Java re-implementation of Michael Eisen's TreeView

Treeviewx

Displays and prints phylogenetic trees

Debian packages in contrib or non-free

Beast-mcmc

Bayesian MCMC phylogenetic inference

Gmap

spliced and SNP-tolerant alignment for mRNA and short reads

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

Forester

Graphical vizualiation tool Archaeopteryx

Jmodeltest

HPC selection of models of nucleotide substitution

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

Acedb-other

recuperação de DNA ou sequências de proteínas

Aevol

digital genetics model to run Evolution Experiments in silico

Alien-hunter

Temas de Ordem Variável Interpolados para identificar DNA adquirido horizontalmente

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

análise das ligações do ligante à estrutura de proteína

Autodock-vina

docking of small molecules to proteins

Autogrid

pré-calcula ligações de ligantes aos seus receptores

Bamtools

toolkit for manipulating BAM (genome alignment) files

Bedtools

suite of utilities for comparing genomic features

Biomaj

biological data-bank updater

Bioperl

Ferramentas Perl para biologia molecular computacional

Bioperl-run

BioPerl wrappers: scripts

Biosquid

utilities for biological sequence analysis

Blast2

Basic Local Alignment Search Tool ("Fer. Básica de Busca de Alinhamento Local")

Bowtie

Ultrafast memory-efficient short read aligner

Bowtie2

ultrafast memory-efficient short read aligner

Boxshade

embelezador de impressão de alinhamentos de seqüência múltipla

Bwa

Burrows-Wheeler Aligner

Cain

simulations of chemical reactions

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

alinhador de seqüências múltiplas baseado em segmentos

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

Fastx-toolkit

FASTQ/A short nucleotide reads pre-processing tools

Filo

FILe and stream Operations

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

produz saída PostScript gráfica a partir de arquivos GFF

Giira

RNA-Seq driven gene finding incorporating ambiguous reads

Glam2

gapped protein motifs from unaligned sequences

Grinder

Versatile omics shotgun and amplicon sequencing read simulator

Gromacs

simulador de dinâmica molecular, com ferramentas de construção e análise

Hhsuite

sensitive protein sequence searching based on HMM-HMM alignment

Hmmer

perfis "hidden Markov models" para análise de seqüência de proteína

Idba

iterative De Bruijn Graph De Novo short read assembler for transcriptome

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

alinhamento eficiente de seqüência para genomas completos

Muscle

programa de alinhamento múltiplo de sequências de proteína

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

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

ferramenta para desenhar acompanhamento de oligo nucleotídeos para amplificação de DNA

Probabel

Toolset for Genome-Wide Association Analysis

Probcons

PROBabilistic CONSistency-based multiple sequence alignment

Proda

alinhamento múltiplo de seqüências de proteína

Prodigal

Microbial (bacterial and archaeal) gene finding program

Pynast

alignment of short DNA sequences

Python-biopython

Python library for bioinformatics (implemented in Python 2)

Python-cogent

framework for genomic biology

Python3-biopython

Python library for bioinformatics (implemented in Python 3)

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 and BAM formats

Seqan-apps

C++ library for the analysis of biological sequences

Sibsim4

seqüências de RNA expressadas em alinhamento em um modelo de DNA

Sigma-align

Simple greedy multiple alignment of non-coding DNA sequences

Sim4

ferramenta para alinhamento cDNA e DNA genômico

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 maniuplating 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

Tophat

fast splice junction mapper for RNA-Seq reads

Tree-ppuzzle

reconstrução paralelizada de árvores filogenéticas por máxima probabilidade

Tree-puzzle

reconstrução de árvores filogenéticas por máxima probabilidade

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

Abyss

de novo, parallel, sequence assembler for short reads

Cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq

Embassy-phylip

EMBOSS conversions of the programs in the phylip package

Gmap

spliced and SNP-tolerant alignment for mRNA and short reads

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

Bagpipe

genomewide LD mapping

R-other-valdar-bagphenotype.library

GNU R extension of the functionality of happy

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

Zope-zms

Content management for science, technology and medicine

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

Xnat

platform for data management and productivity tasks in neuroimaging

No known packages available

Hid

database management system for clinical imaging

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

Python-hl7

Python library for parsing HL7 messages

Official Debian packages with lower relevance

Sleepyhead

Sleep tracking software with a focus on monitoring CPAP treatment

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

This library generates images of teeth for odontograms.

Openmolar

dental practice management software

Epidemiology - pacotes relacionados a epidemiologia do Debian Med

Este meta-pacote vai instalar ferramentas úteis em pesquisa epidemiológica. Muitos pacotes fazem uso da linguagem de dados GNU R para investigação estatística. É uma boa ideia ler o artigo "A short introduction to R for Epidemiology" em http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf

Official Debian packages with high relevance

Epigrass

ferram. científica p/ simul. e análise de cenários em rede epidemológica

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

calculadora epidemiológica GNU R

R-cran-epir

funções GNU R para análise de dados epidemiológicos

R-cran-epitools

ferramentas epidemiológicas para dados e gráficos GNU R

R-cran-seroincidence

GNU R seroincidence calculator tool

R-cran-surveillance

GNU R package for the Modeling and Monitoring of Epidemic Phenomena

Official Debian packages with lower relevance

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

Netepi-analysis

network-enabled tools for epidemiology and public health practice

Netepi-collection

network-enabled tools for epidemiology and public health practice

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

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

Care2x

integrated hospital information system

Ewd-920

package for EWD Entrerprise Web Development platform.

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 - pacotes de imagens Debian Med

Este meta pacote irá instalar pacotes Debian que podem ser úteis no processamento de imagens médicas.

Ele instala diversos pacotes que suportam DICOM (Digital Imaging and Communications in Medicine, ou em português, Comunicações e Imagens Digitais na Medicina) que é o padrão de fato, para gerenciamento de imagens médicas. O padrão define estruturas de dados e serviços para a troca de imagens médicas e informações relacionadas. O último lançamento foi em 2008 e consiste em 18 partes.

Para mais informações, você pode visitar o site web do NEMA http://medical.nema.org/ .

A situação do padrão base DICOM oficial mais todos os suplementos e itens de correção estão resumidos no site web de David Clunie: http://www.dclunie.com/dicom-status/status.html where você encontrará links diretos para a edição anual mais recente ftp://medical.nema.org/medical/dicom/2008/ .

Official Debian packages with high relevance

Aeskulap

visualizador de imagem médica e cliente de rede DICOM

Amide

software for Medical Imaging

Ants

advanced normalization tools for brain and image analysis

Bart

tools for computational magnetic resonance imaging

Biosig-tools

format conversion tools for biomedical data formats

Camitk-imp

aplicativo de banco de testes para a biblioteca CamiTK

Caret

Computerized Anatomical Reconstruction and Editing Toolkit

Conquest-common

ConQuest DICOM Server - common files

Ctn

Central Test Node, uma implementação do DICOM para medicina por imagem

Ctsim

simulador de tomografia computadorizada

Dcmtk

OFFIS DICOM toolkit command line utilities

Dicom3tools

DICOM medical image files manipulation and conversion tools

Dicomnifti

converte arquivos DICOM em formato NIfTI

Dicomscope

OFFIS DICOM Viewer

Fslview

visualizador para dados (f)MRI e DTI

Fw4spl

FrameWork for Software Production Line

Gdf-tools

IO library for the GDF -- helper tools

Ginkgocadx

Medical Imaging Software and complete DICOM Viewer

Gofigure2

Tool for visualizing, processing and analysing of bioimages

Gwyddion

Scanning Probe Microscopy visualization and analysis tool

Imagej

Image processing program inspired by NIH Image

Imagevis3d

desktop volume rendering application for large data

Invesalius

software de reconstrução de imagens médicas 3D

Ismrmrd-tools

ISMRM Raw Data format (ISMRMRD) - binaries

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

ferramentas para o formato de medicina por imagem MNI

Mriconvert

utilitário para conversão de arquivo de imagem médica

Mricron

magnetic resonance image conversion, viewing and analysis

Mrtrix

diffusion-weighted MRI white matter tractography

Nifti-bin

tools shipped with the NIfTI library

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

Pixelmed-apps

DICOM implementation containing Image Viewer and a ECG Viewer - jnlp

Plastimatch

medical image reconstruction and registration

Python-dicom

DICOM medical file reading and writing (Python 2)

Python-dipy

Python library for the analysis of diffusion MRI datasets

Python-mvpa2

multivariate pattern analysis with Python v. 2

Python-nibabel

Python bindings to various neuroimaging data formats

Python-nipy

Analysis of structural and functional neuroimaging data

Python-nipype

Neuroimaging data analysis pipelines in Python

Python-nitime

timeseries analysis for neuroscience data (nitime)

Python-surfer

visualize Freesurfer's data in Python

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 image and metadata from TIFF, STK, LSM, OME-TIFF and FluoView files

Via-bin

tools for volumetric image analysis

Volview

Advanced volume visualization tool

Voxbo

processing, statistical analysis, and display of brain imaging data

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

programas de manipulação de imagens -- binários

Imview

aplicação de análise e visualização de imagem

Openwalnut-qt4

Multi-modal medical and brain data visualization tool.

Orthanc-dicomweb

Plugin to extend Orthanc with support of WADO and DICOMweb

Orthanc-imagej

ImageJ plugin to import images from 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

utilitário de otimização de PNG (Portable Network Graphics)

Python-pyxid

interface for Cedrus XID and StimTracker devices

Trimage

GUI and command-line interface to optimize image files

Debian packages in contrib or non-free

Fsl

transitional dummy package

Vmtk

the Vascular Modeling Toolkit

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

Afni

toolkit for analyzing and visualizing functional MRI data

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

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

Xnat

platform for data management and productivity tasks in neuroimaging

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 - pacotes Debian Med para desenvolvimento de imagens médicas

Este meta pacote instalará pacotes Debian que poderão ser úteis para o desenvolvimento de aplicações para o processamento de imagens médicas.

Official Debian packages with high relevance

Cimg-dev

poderosa biblioteca de processamento de imagens

Ctn-dev

arquivos de desenvolvimento p/ Central Test Node, uma implementação do DICOM

Gmic

GREYC's Magic for Image Computing

Libactiviz.net-cil

Tool for generating C# wrappers around VTK

Libbart-dev

Development files for BART

Libbiosig-dev

I/O library for biomedical data - development files

Libcamitk3-dev

Computer Assisted Medical Intervention Tool Kit - development

Libcv-dev

Translation package for libcv-dev

Libedf-dev

European Data Format library - devel

Libgdf-dev

IO library for the GDF -- development library

Libgiftiio-dev

biblioteca de IO (ES - Entrada e Saída) para o formato de dados de superfície cortical GIFTI

Libigstk4-dev

Toolkit for image-guided surgery applications - development

Libinsighttoolkit4-dev

"toolkit" processamento de imagens p/ registro e segmentação - desenvolvimento

Libismrmrd-dev

ISMRM Raw Data format (ISMRMRD) - development files

Libmaxflow-dev

Development files for the maxflow-mincut algorithm

Libmdc2-dev

Medical Image (DICOM, ECAT, ...) conversion tool (development)

Libmia-2.2-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

Libnifti-dev

IO libraries for the NIfTI-1 data format

Libodil0-dev

Odil is a C++11 library for the DICOM standard (development files)

Libopenigtlink1-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

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-java

DICOM for VTK - java

Libvtk-dicom0.5-dev

DICOM for VTK - dev

Libvtk6-dev

VTK header files

Libvxl1-dev

C++ Libraries for Computer Vision Research (development files)

Octave-bart

Octave bindings for BART

Octave-gdf

IO library for the GDF -- Octave interface

Odin

develop, simulate and run magnetic resonance sequences

Python-casmoothing

Context-aware mesh smoothing for biomedical applications

Python-cfflib

Multi-modal connectome and metadata management and integration

Python-dicom

DICOM medical file reading and writing (Python 2)

Python-dipy

Python library for the analysis of diffusion MRI datasets

Python-gdcm

Grassroots DICOM Python bindings

Python-mia

Python-2 bindings for the MIA image processing library

Python-mne

Python modules for MEG and EEG data analysis

Python-mvpa2

multivariate pattern analysis with Python v. 2

Python-nibabel

Python bindings to various neuroimaging data formats

Python-nipy

Analysis of structural and functional neuroimaging data

Python-nipype

Neuroimaging data analysis pipelines in Python

Python-nitime

timeseries analysis for neuroscience data (nitime)

Python-openslide

Python 2 wrapper for reading whole slide image files

Python-pyxnat

Interface to access neuroimaging data on XNAT servers

Python-vigra

Python bindings for the C++ computer vision library

Python3-mia

Python-3 bindings for the MIA image processing library

R-cran-rniftilib

GNU/R interface to NIFTICLIB

Official Debian packages with lower relevance

Igstk-examples

Toolkit for image-guided surgery applications - examples

Libcamp0.7-dev

C++ multi-purpose reflection library (development files)

Libeegdev-dev

Biosignal acquisition device library (Developement files)

Libfreeimage-dev

Support library for graphics image formats (development files)

Libics-dev

Image Cytometry Standard file reading and writing

Liblimereg-dev

Library for lightweight image registration [development files]

Libnifti-doc

documentação da API da biblioteca NIfTI

Libvtkedge-dev

Library of advanced visualization and data processing techniques - development

Libxdffileio-dev

Library to read/write EEG data file formats (development files)

Python-libavg

High-level development platform for media-centric applications

Python-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

Debian packages in experimental

Libctk-dev

toolkit for medical imaging application development - devel

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

Libopenslide-java

java wrapper for reading whole slide image files

Python-imageio

Library for reading and writing a wide range of image formats (Python 2)

Unofficial packages built by somebody else

Libmni-perllib-perl

The MNI Perl Library

No known packages available

Octave-dicom

Dicom support in Octave

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

No known packages available

Catissuesuite

tool for biospecimen inventory management

Openelis

Enterprise Laboratory Information System

Openfreezer

Laboratory analysis, research and investigation software application

Oncology - Debian Med packages for oncology

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

Official Debian packages with high relevance

Dicompyler

plataforma de pesquisa em radioterapia

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

programa para desenho de estruturas químicas

R-cran-dosefinding

Planning and Analyzing Dose Finding experiments

Debian packages in contrib or non-free

Raccoon

preparation of in silico drug screening projects

Physics - pacotes Debian Med para médicos

Este meta-pacote contém dependências para uma coleção de software e documentação que é útil para médicos em oncologia de radiação, de diagnóstico por imagem e áreas afins.

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

linguagem Octave da GNU para cáculos numéricos

Paw

Physics Analysis Workstation - um programa de análise gráfica

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 exemplos e testes

Python-biosig

Python bindings for BioSig library

Python-multipletau

multiple-tau algorithm for Python/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 - pacotes Debian Med para gerenciamento de consultórios

Este metapacote contém dependências para uma coleção de softwares que podem ser úteis para profissionais liberais gerenciarem seus consultórios.

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

gerenciamento de consultório médico - servidor

Libchipcard-tools

ferramentas para acesso a cartões com chip

Qrisk2

cardiovascular disease risk calculator

R-cran-medadherence

GNU R Adesão Medicamentosa: definições comumente usadas

Sleepyhead

Sleep tracking software with a focus on monitoring CPAP treatment

Official Debian packages with lower relevance

Libctapimkt1

Read German Krankenversichertenkarte and eGK

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

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

Freeshim

opensource electronic medical device interface

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

Python-pyepl

module for coding psychology experiments in Python

Python-pypsignifit

psychometric analysis of psychophysics data in Python

R-cran-foreign

GNU R package to read/write data from other stat. systems

R-cran-psy

GNU R procedures for psychometrics

Official Debian packages with lower relevance

Python-visionegg

Python library for 2D/3D visual stimulus generation

Science-psychophysics

Debian Science packages for Psychophysics

Unofficial packages built by somebody else

Miscpsycho

Miscellaneous Psychometric Analyses

Psych

Procedures for Psychological, Psychometric, and Personality Research

Psychometric

Applied Psychometric Theory

Psychotree

Recursive Partitioning Based on Psychometric Models

Psyphy

Functions for analyzing psychophysical data in R

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.

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

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

Hunspell-de-med

dicionário médico para o hunspell

Hunspell-en-med

English medical dictionary for hunspell

Nut-nutrition

dietary nutrition analysis software

Pcalendar

acompanha os ciclos menstruais e prevê os períodos de fertilidade

Pondus

personal weight manager for GTK+2

Python-clips

Python module to interface the CLIPS expert system shell library

Python-fitbit

FitBit REST API Client Implementation

Quitcount

Small tool which may help yourself quit smoking

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

Sleepyhead

Sleep tracking software with a focus on monitoring CPAP treatment

Debian packages in contrib or non-free

Mssstest

Normalisation of disease scores for patients with Multiple Sclerosis

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: Natural and computer sciences

Official Debian packages with lower relevance

Biber

Much-augmented BibTeX replacement for BibLaTeX users

Bibus

banco de dados bibliográfico

Jabref-plugin-oo

LibreOffice plugin for JabRef (transitional dummy package)

Kbibtex

BibTeX editor for KDE

Referencer

GNOME Document Organiser