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

Ce méta-paquet installera les paquets qui sont utiles pour faire des statistiques avec un accent particulier sur les tâches dans les soins médicaux.

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-limma
modèles linéaires pour des données de puce (microarray)
Versions of package r-bioc-limma
ReleaseVersionArchitectures
jessie3.22.1+dfsg-1amd64,armel,armhf,i386
buster3.38.3+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch3.30.8+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy3.12.0~dfsg-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid3.38.3+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream3.40.2
Popcon: 14 users (10 upd.)*
Newer upstream!
License: DFSG free
Git

Il s’agit d’un programme du projet Bioconductor pour l’analyse de données d’expression de gènes de puce (microarray), particulièrement avec l’utilisation de modèles linéaires pour l’analyse de conception d’expériences et l’évaluation d’expression différentielle. Le paquet fournit des possibilités de pré-traitement pour les puces décolorées en deux couleurs. Les méthodes d’expression différentielle s’appliquent à toutes les plateformes de puce et traitent les expérimentations simple canal et double canaux d’Affymetrix, de manière unifiée.

Please cite: Gordon K. Smyth: Limma: linear models for microarray data. (eprint) :397-420 (2005)
Registry entries: Bio.Tools  SciCrunch  OMICtools 
R-bioc-multtest
Bioconductor resampling-based multiple hypothesis testing
Versions of package r-bioc-multtest
ReleaseVersionArchitectures
sid2.38.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch2.30.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.38.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream2.40.0
Popcon: 6 users (3 upd.)*
Newer upstream!
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
paquet de GNU R pour une estimation de valeurs-q pour le contrôle FDR
Versions of package r-bioc-qvalue
ReleaseVersionArchitectures
sid2.14.1-1all
wheezy1.30.0-1all
jessie1.40.0-1all
stretch2.6.0-1all
buster2.14.1-1all
upstream2.16.0
Popcon: 12 users (3 upd.)*
Newer upstream!
License: DFSG free
Git

Ce paquet prend une liste de valeurs-p résultant du test simultané de plusieurs hypothèses et calcule leurs valeurs-q. La valeur-q d’un test mesure la proportion de faux positifs (appelé false discovery rate — taux de fausses découvertes) occasionnée quand un test particulier est dit significatif. Divers tracés sont automatiquement générés, permettant de dégager des niveaux de seuil pertinents. Plusieurs résultats mathématiques ont récemment montré la précision conservative des valeurs-q estimées à partir de ce logiciel. Ce logiciel peut être utilisé pour des problèmes de génomique, d’imagerie cérébrale, d’astrophysique ou d’exploration de données.

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
buster1.7-13-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.7-5-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.7-13-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 15 users (7 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
tracé de points « bee swarm », une alternative au tracé « stripchart »
Versions of package r-cran-beeswarm
ReleaseVersionArchitectures
jessie0.1.6-2all
stretch0.2.3-1all
buster0.2.3-3all
sid0.2.3-3all
Popcon: 8 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Beeswarm est un paquet d’extension pour R, l’environnement de statistiques. Le tracé « bee swarm » est un tracé en nuage de points à une dimension ressemblant au tracé « stripchart », mais plus étroitement groupé, sans chevauchement de points.

R-cran-pvclust
Hierarchical Clustering with P-Values via Multiscale Bootstrap
Versions of package r-cran-pvclust
ReleaseVersionArchitectures
jessie1.3-0-1all
stretch2.0-0-1all
buster2.0-0-4all
sid2.0-0-4all
wheezy1.2-2-1all
Popcon: 13 users (4 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)
Registry entries: OMICtools 
R-cran-randomforest
paquet de GNU R mettant en œuvre le classificateur de forêts aléatoires
Versions of package r-cran-randomforest
ReleaseVersionArchitectures
wheezy4.6-6-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid4.6-14-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster4.6-14-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch4.6-12-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie4.6-10-1amd64,armel,armhf,i386
squeeze4.5-34-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package r-cran-randomforest:
devellang:r, library
fieldbiology, biology:bioinformatics, medicine
interfacecommandline
roledevel-lib, shared-lib
Popcon: 25 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

RandomForest met en œuvre l’algorithme des forêts d'arbres décisionnels (ou forêts aléatoires) de Breiman (en se basant sur le code original écrit en Fortran de Breiman et Cutler) pour la classification et la régression. Il peut être aussi utilisé dans le mode non surveillé (unsupervised) pour l’évaluation des proximités entre les points de données.

La technique utilise plusieurs arbres de décision et combine leurs votes individuels.

R-cran-rwave
GNU R time-frequency analysis of 1-D signals
Versions of package r-cran-rwave
ReleaseVersionArchitectures
sid2.4-8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.4-8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 6 users (1 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
buster1.84-6.1-2all
sid1.84-6.1-2all
Popcon: 4 users (0 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
sid1.7.5.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.7.5.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 6 users (0 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
sid4.6.8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster4.6.8-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 6 users (0 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
paquets pour les statistiques de Debian Science
Versions of package science-statistics
ReleaseVersionArchitectures
wheezy1.0all
jessie1.4all
stretch1.7all
buster1.9all
sid1.10all
squeeze0.12all
Debtags of package science-statistics:
rolemetapackage
suitedebian
Popcon: 20 users (9 upd.)*
Versions and Archs
License: DFSG free
Git

Ce paquet fait partie du mélange exclusif « Debian Science » et installe les paquets concernant les statistiques. Cette tâche est une tâche générale pouvant être utile pour n’importe quels travaux scientifiques. Elle dépend de beaucoup de paquets R ainsi que d’autres outils utiles pour faire des statistiques. De plus la tâche « Science Mathematics » est suggérée pour installer facultativement tous les logiciels relatifs aux mathématiques.

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

Rstudio
GNU R IDE
Versions of package rstudio
ReleaseVersionArchitectures
VCS0.99.1168+dfsg-1all
Versions and Archs
License: <license>
Debian package not available
Git
Version: 0.99.1168+dfsg-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 195839