Debian Med Project
Help us to see Debian used by medical practitioners and biomedical researchers! Join us on the Salsa page.
Summary
Statistics
Debian Med - Statistik

Dieses Metapaket installiert Pakete, die hilfreich sind für Statistik mit einem speziellen Fokus auf Aufgaben in der medizinischen Versorgung.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Statistics packages

Official Debian packages with high relevance

r-bioc-edger
Empirische Analyse von digitalen Genexpressionsdaten mit R
Versions of package r-bioc-edger
ReleaseVersionArchitectures
jessie3.8.2+dfsg-1amd64,armel,armhf,i386
trixie4.0.15+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid4.0.15+dfsg-1armel,armhf
bookworm3.40.2+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.32.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid4.0.16+dfsg-1amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x
stretch3.14.0+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 18 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Bioconductor-Paket zur Differentialexpressionsanalyse eines vollkommen sequenzierten Transkriptom (RNA-seq) und digitalen Genexpressionsprofilen mit biologischer Replikation. Es verwendet empirische Bayes-Methoden und exakte Tests, die auf der negativen Binomialverteilung basieren. Es ist auch für die Differentialsignalanalyse mit anderen Typen von Zähldaten in der Größenordnung von Genomen verwendbar.

Please cite: Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. (PubMed,eprint) Bioinformatics 26,:139-140 (2010)
Registry entries: Bio.tools  SciCrunch  Bioconda 
r-bioc-limma
linear models for microarray data
Versions of package r-bioc-limma
ReleaseVersionArchitectures
trixie3.58.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
jessie3.22.1+dfsg-1amd64,armel,armhf,i386
stretch3.30.8+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.38.3+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.46.0+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.58.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm3.54.1+dfsg-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 19 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

Microarrays are microscopic plates with carefully arranged short DNA strands and/or chemically prepared surfaces to which other DNA preferably binds. The amount of DNA binding at different locations of these chips, typically determined by a fluorescent dye, is to be interpreted. The technology is typically used with DNA that is derived from RNA, i.e to determine the activity of a gene and/or its splice variants. But the technology is also used to determine sequence variations in genomic DNA.

This Bioconductor package supports the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The package includes pre-processing capabilities for two-colour spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way.

Please cite: Gordon K. Smyth: Limma: linear models for microarray data. (eprint) :397-420 (2005)
Registry entries: Bio.tools  SciCrunch  Bioconda 
r-bioc-multtest
Bioconductor resampling-based multiple hypothesis testing
Versions of package r-bioc-multtest
ReleaseVersionArchitectures
sid2.58.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie2.58.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
bullseye2.46.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch2.30.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bookworm2.54.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.38.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 7 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

r-bioc-qvalue
»GNU R«-Paket zur Q-Wert-Bestimmung für FDR-Steuerung
Versions of package r-bioc-qvalue
ReleaseVersionArchitectures
sid2.34.0-1all
jessie1.40.0-1all
bookworm2.30.0-1all
trixie2.34.0-1all
stretch2.6.0-1all
buster2.14.1-1all
bullseye2.22.0-1all
Popcon: 8 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

Dieses Paket liefert eine Liste von p-Werten resultierend aus simultanen Tests von vielen Hypothesen und schätzt deren q-Werte. Der q-Wert eines Tests misst die Kosten der Proportionen von Falsch-zu-Richtig (genannt die »false discovery rate«, Fehlerentdeckungsrate), wenn der einzelne Test signifikant ist. Es werden automatisch unterschiedliche Aufzeichnungen generiert, die es einem Einzelnen erlauben ausschlaggebende »Cut-Off«-Werte zu liefern. Mehrere mathematische Ergebnisse haben in der Vergangenheit die konservative Genauigkeit der geschätzten q-Werte dieser Software gezeigt. Das Programm kann zur Problemlösung bei Genomik, Bildgebung des Gehirns, Astrophysik und Data Mining angewendet werden.

Please cite: John D Storey and Robert Tibshirani: Statistical significance for genomewide studies. (PubMed,eprint) Proceedings of the National Academy of Sciences of the United States of America 100(16):9440-9445 (2003)
r-cran-ade4
GNU R analysis of ecological data
Versions of package r-cran-ade4
ReleaseVersionArchitectures
bullseye1.7-16-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.7-22-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.7-22-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid1.7-22-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch1.7-5-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.7-13-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 21 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

This GNU R package allows analysis of ecological data and contains exploratory and euclidean methods in environmental sciences.

It supports multivariate data analysis and graphical display.

Please cite: Stéphane Dray and Anne-Béatrice Dufour: The ade4 Package: Implementing the Duality Diagram for Ecologists. (eprint) Journal of Statistical Software 22(4):1-20 (2007)
r-cran-beeswarm
bee swarm plot, an alternative to stripchart
Versions of package r-cran-beeswarm
ReleaseVersionArchitectures
stretch0.2.3-1all
jessie0.1.6-2all
sid0.4.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie0.4.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
bookworm0.4.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.2.3-4all
buster0.2.3-3all
Popcon: 58 users (24 upd.)*
Versions and Archs
License: DFSG free
Git

Beeswarm is an add-on package for the R statistical environment. The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.

r-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
Versions of package r-cran-pvclust
ReleaseVersionArchitectures
jessie1.3-0-1all
trixie2.2-0-2all
bookworm2.2-0-2all
bullseye2.2-0-2all
sid2.2-0-2all
buster2.0-0-4all
stretch2.0-0-1all
Popcon: 52 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

pvclust is a package for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-values as well as BP (boostrap probability) values computed via multiscale bootstrap resampling.

Please cite: Ryota Suzuki and Hidetoshi Shimodaira: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. (PubMed,eprint) Bioinformatics 22(12):1540-1542 (2006)
r-cran-randomforest
GNU-R-Paket, das den Klassifikator Random Forest implementiert
Versions of package r-cran-randomforest
ReleaseVersionArchitectures
stretch4.6-12-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie4.6-10-1amd64,armel,armhf,i386
buster4.6-14-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye4.6-14-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm4.7-1.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie4.7-1.1-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid4.7-1.1-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package r-cran-randomforest:
devellang:r, library
fieldbiology, biology:bioinformatics, medicine
interfacecommandline
roledevel-lib, shared-lib
Popcon: 66 users (17 upd.)*
Versions and Archs
License: DFSG free
Git

RandomForest implementiert Breimans Random-Forest-Algorithmus (basierend auf dem ursprünglichen Fortran-Code von Breiman und Cutler) zur Klassifikation und Regression. Es kann auch im nicht überwachten Modus verwendet werden, um die Nähe von Datenpunkten zu bemessen.

Diese Technik verwendet multiple Entscheidungsbäume und kombiniert deren individuelle Stimmen.

r-cran-rwave
GNU R time-frequency analysis of 1-D signals
Versions of package r-cran-rwave
ReleaseVersionArchitectures
bullseye2.4-8-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm2.6-5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.6-5-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid2.6-5-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster2.4-8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

A set of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani (1998, eBook ISBN:978008053942), Academic Press.

r-cran-snowfall
GNU R easier cluster computing (based on snow)
Versions of package r-cran-snowfall
ReleaseVersionArchitectures
trixie1.84-6.3-1all
bookworm1.84-6.2-1all
bullseye1.84-6.1-3all
buster1.84-6.1-2all
sid1.84-6.3-1all
Popcon: 7 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

r-cran-waveslim
GNU R wavelet routines for 1-, 2- and 3-D signal processing
Versions of package r-cran-waveslim
ReleaseVersionArchitectures
trixie1.8.4-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
bookworm1.8.4-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.8.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.7.5.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.8.4-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Popcon: 5 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.

r-cran-wavethresh
GNU R wavelets statistics and transforms
Versions of package r-cran-wavethresh
ReleaseVersionArchitectures
sid4.7.2-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster4.6.8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye4.6.8-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie4.7.2-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
bookworm4.7.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 6 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Official Debian packages with lower relevance

science-statistics
»Debian Science« Statistik-Pakete
Versions of package science-statistics
ReleaseVersionArchitectures
trixie1.14.5all
sid1.14.5all
stretch1.7all
jessie1.4all
buster1.10all
bullseye1.14.2all
bookworm1.14.5all
Debtags of package science-statistics:
rolemetapackage
suitedebian
Popcon: 5 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Dieses Metapaket ist Teil des Debian Pure Blend »Debian Science« und installiert Pakete im Zusammenhang zum Begriff Statistiken. Dieser Task ist ein allgemeiner Task, welcher nützlich ist für alle wissenschaftlichen Arbeiten. Das Paket hängt von einer Reihe von R-Paketen ab, genau so wie von anderen Werkzeugen, die nützlich für die Anwendung von Statistik sind. Des weiteren ist der Task Mathematik-Wissenschaften empfohlen, um optionale Mathematik-Software zu installieren.

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

rstudio
GNU R IDE
Versions of package rstudio
ReleaseVersionArchitectures
VCS2022.07.1+554-1all
Versions and Archs
License: AGPL-3.0
Debian package not available
Git
Version: 2022.07.1+554-1

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 236867