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Package Usage: cran: ashr

Methods for Adaptive Shrinkage, using Empirical Bayes
7 versions
Latest release: over 2 years ago
8 dependent packages
3,258 downloads last month

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ashr

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/stephens999%2Fashr

Dependent Repos 33

UMMS-Biocore/debrowser
Differential Count Data Analysis Toolbox
  • * DESCRIPTION

Size: 38.7 MB - Last synced: 30 days ago - Pushed: 4 months ago

stephens999/dscr
Dynamic statistical comparisons in R
  • * DESCRIPTION

Size: 802 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago

stephenslab/ebnm
R package to fit Empirical Bayes Normal Means model.
  • * DESCRIPTION

Size: 6.78 MB - Last synced: 1 day ago - Pushed: 1 day ago

thelovelab/DESeq2
Differential expression of RNA-seq data using the Negative Binomial
  • * DESCRIPTION

Size: 3.67 MB - Last synced: 19 days ago - Pushed: about 2 months ago

stephenslab/fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
  • * DESCRIPTION

Size: 149 MB - Last synced: 1 day ago - Pushed: 2 months ago

acidgenomics/r-deseqanalysis
Toolkit for performing differential expression with DESeq2.
  • * DESCRIPTION

Size: 47.9 MB - Last synced: 2 months ago - Pushed: 2 months ago

pbreheny/ncvreg
Regularization paths for SCAD- and MCP-penalized regression models
  • * DESCRIPTION

Size: 3.26 MB - Last synced: 2 days ago - Pushed: 2 days ago

r-pkg-team/r-bioc-deseq2
r-bioc-deseq2 packaging
  • * DESCRIPTION

Last synced: over 1 year ago

rauschenberger/palasso
Paired Lasso Regression
  • * DESCRIPTION

Size: 1.81 MB - Last synced: 4 months ago - Pushed: 4 months ago

guillaumecharbonnier/colab-r-libs
A test to see how I could save installation time for R libs each time I start a Colab notebook
  • * DESeq2/DESCRIPTION

Size: 156 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

biospi/bayesprot
DEPRECATED - Bayesian linear mixed-effects model for protein-level quantification in proteomics
  • >= 2.2 DESCRIPTION

Size: 12.2 MB - Last synced: 8 months ago - Pushed: over 4 years ago

broadinstitute/cdsr_biomarker
R toolkit for biomarker analysis
  • * DESCRIPTION

Size: 419 KB - Last synced: almost 1 year ago - Pushed: almost 2 years ago

stephenslab/mashr
An R package for multivariate adaptive shrinkage.
  • >= 2.2 DESCRIPTION

Size: 49.2 MB - Last synced: 15 days ago - Pushed: 8 months ago

pbreheny/breheny
  • * DESCRIPTION

Size: 13.8 MB - Last synced: 1 day ago - Pushed: 1 day ago

PF2-pasteur-fr/SARTools
Statistical Analysis of RNA-Seq Tools
  • >= 2.2 DESCRIPTION

Size: 2.17 MB - Last synced: 7 months ago - Pushed: 12 months ago

broadinstitute/cdsr_models
Univariate and multivariate models multi-omic analyses
  • * DESCRIPTION

Size: 324 KB - Last synced: almost 1 year ago - Pushed: almost 2 years ago

stephenslab/multiseq
Development of software and methods for analysis of sequence data from multiple samples
  • * package/multiseq.Rcheck/00_pkg_src/multiseq/DESCRIPTION

Size: 78.4 MB - Last synced: 8 months ago - Pushed: over 7 years ago

MicrobialGenomics-IrsicaixaOrg/dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
  • * DESCRIPTION

Size: 38.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

jean997/cause
R package for CAUSE
  • * DESCRIPTION

Size: 101 MB - Last synced: 5 months ago - Pushed: 5 months ago

blaserlab/blaseRtools
R Tools for Blaser Lab Data Analysis
  • * DESCRIPTION

Size: 68.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

UMMS-Biocore/dprofiler
  • * DESCRIPTION

Size: 556 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

weversMJW/pseude
Aggregate single-cell level gene counts, run DESeq2
  • * DESCRIPTION

Size: 47.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

mengyin/vashr
An R package for variance adaptive shrinkage
  • * DESCRIPTION

Size: 115 KB - Last synced: over 1 year ago - Pushed: almost 7 years ago

cran/ncvreg
:exclamation: This is a read-only mirror of the CRAN R package repository. ncvreg — Regularization Paths for SCAD and MCP Penalized Regression Models. Homepage: https://pbreheny.github.io/ncvreg/, https://github.com/pbreheny/ncvreg Report bugs for this package: https://github.com/pbreheny/ncvreg/issues
  • * DESCRIPTION

Size: 1000 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

hugheylab/limorhyde2
  • >= 2.2 DESCRIPTION

Size: 25.2 MB - Last synced: 21 days ago - Pushed: 6 months ago

dcgerard/ldsep
Linkage Disequilibrium Shrinkage Estimation for Polyploids
  • * DESCRIPTION

Size: 3.97 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

dcgerard/succotashr
Implement SUCCOTASH for accounting for hidden variables in large scale gene expression studies.
  • * DESCRIPTION

Size: 177 KB - Last synced: over 1 year ago - Pushed: over 7 years ago

MoTrPAC/MotrpacRatTraining6mo
Analysis of the MoTrPAC endurance exercise training study in 6-month-old rats
  • * DESCRIPTION

Size: 80.7 MB - Last synced: 7 months ago - Pushed: 7 months ago

stephenslab/fsusieR
Draft package for "Sum of Single Functions" method.
  • >= 2.2 DESCRIPTION

Size: 37.4 MB - Last synced: 3 months ago - Pushed: 3 months ago

lgarreta/multigwas-dev
Tool for GWAS on tetraploid species using multiple GWAS tools (development release)
  • * opt/Rlibs/ldsep/DESCRIPTION

Size: 488 MB - Last synced: over 1 year ago

vishalbelsare/mashr Fork of stephenslab/mashr
An R package for multivariate adaptive shrinkage.
  • >= 2.2 DESCRIPTION

Size: 49.2 MB - Last synced: 8 days ago - Pushed: 8 months ago

stephenslab/smashr
An R package for smoothing & signal denoising using adaptive shrinkage.
  • * DESCRIPTION

Size: 1.37 MB - Last synced: 10 months ago - Pushed: almost 3 years ago

cran/CorShrink
:exclamation: This is a read-only mirror of the CRAN R package repository. CorShrink — Adaptive Shrinkage of Correlation and Covariance Matrices. Homepage: https://github.com/kkdey/CorShrink Report bugs for this package: http://github.com/kkdey/CorShrink/issues
  • * DESCRIPTION

Size: 6.37 MB - Last synced: 10 months ago - Pushed: almost 6 years ago

pfh/topconfects
TOP results by CONfident efFECT Sizes.
  • * DESCRIPTION

Size: 608 KB - Last synced: 18 days ago - Pushed: 7 months ago

stephenslab/mvsusieR
A new model and algorithm for multivariate Bayesian variable selection regression.
  • * DESCRIPTION

Size: 39.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

Ghoshlab/cytoKernel
R package for differential expression analyses of high-dimensional biological data
  • * DESCRIPTION

Size: 249 KB - Last synced: 6 months ago - Pushed: over 2 years ago

stephenslab/miximash
MIXtures of Independent components in Multivariate Adaptive SHrinkage ("miximash").
  • >= 2.1 DESCRIPTION

Size: 394 KB - Last synced: 10 months ago - Pushed: over 6 years ago

stephenslab/mvf.susie.alpha
R package implementing multivariate functional susie.
  • >= 2.2 DESCRIPTION

Size: 195 KB - Last synced: 10 months ago - Pushed: over 1 year ago

stephenslab/poisson.mash.alpha
An R package for Poisson multivariate adaptive shrinkage.
  • * DESCRIPTION

Size: 220 MB - Last synced: 6 months ago - Pushed: 6 months ago

cran/palasso
:exclamation: This is a read-only mirror of the CRAN R package repository. palasso — Paired Lasso Regression. Homepage: https://github.com/rauschenberger/palasso Report bugs for this package: https://github.com/rauschenberger/palasso/issues
  • * DESCRIPTION

Size: 210 KB - Last synced: 4 months ago - Pushed: 4 months ago

cran/fastTopics
:exclamation: This is a read-only mirror of the CRAN R package repository. fastTopics — Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data. Homepage: https://github.com/stephenslab/fastTopics Report bugs for this package: https://github.com/stephenslab/fastTopics/issues
  • * DESCRIPTION

Size: 4.52 MB - Last synced: 5 months ago - Pushed: 5 months ago

stephens999/multiseq Fork of stephenslab/multiseq
Development of software and methods for analysis of sequence data from multiple samples
  • * package/multiseq/DESCRIPTION

Size: 63.6 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

RockefellerUniversity/Genomic_HeatmapsAndProfiles
  • * GenomicHeatmaps/DESCRIPTION

Size: 75.7 MB - Last synced: over 1 year ago - Pushed: almost 4 years ago

dcgerard/stramash
ASH but using a mixture likelihood.
  • * DESCRIPTION

Size: 257 KB - Last synced: over 1 year ago - Pushed: almost 8 years ago

dcgerard/unleash
UNimodally Leveraging Empirical-null with Adaptive SHrinkage
  • * DESCRIPTION

Size: 4.88 KB - Last synced: over 1 year ago - Pushed: about 7 years ago

dcgerard/vicar
Various Ideas for Confounder Adjustment in Regression
  • * DESCRIPTION

Size: 10.3 MB - Last synced: 7 months ago - Pushed: about 1 year ago

NKweiwang/flash
just a test
  • * DESCRIPTION

Size: 8.79 KB - Last synced: over 1 year ago - Pushed: over 8 years ago

william-denault/mvf.susie.alpha
draft of mvfsusie
  • >= 2.2 DESCRIPTION

Size: 13.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

paulklemm/dereportr
Differential Gene Expression Analysis based on Salmon output of nf-core RNASeq pipeline
  • * DESCRIPTION

Size: 104 KB - Last synced: about 2 months ago - Pushed: 8 months ago

VincentAlcazer/hemRNA
hemRNA is a free open-source software developed to help clinicians and biologists in analyzing RNAseq data.
  • * DESCRIPTION

Size: 6.33 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

DongyueXie/smashrgen
Smooth Poisson sequence.
  • * DESCRIPTION

Size: 238 KB - Last synced: 6 months ago - Pushed: 6 months ago

kkdey/Logolas
R package for Enrichment Depletion Logos (EDLogos) and String Logos
  • * DESCRIPTION

Size: 21.6 MB - Last synced: 8 months ago - Pushed: over 5 years ago

stephenslab/flashr
R package for Empirical Bayes Factor Analysis.
  • >= 2.2 DESCRIPTION

Size: 1.98 MB - Last synced: 5 months ago - Pushed: 5 months ago

Alice-MacQueen/snpdiver
Exploration of interacting SNP effects in phenotyped mapping populations.
  • * DESCRIPTION

Size: 229 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

Alice-MacQueen/switchgrassGWAS
Genome-wide association on the Panicum virgatum diversity panel.
  • * DESCRIPTION

Size: 60.2 MB - Last synced: 28 days ago - Pushed: over 2 years ago

Alice-MacQueen/CDBNgenomics
Genomics in the Cooperative Dry Bean Nursery
  • * DESCRIPTION

Size: 457 MB - Last synced: 8 months ago - Pushed: almost 4 years ago

mengyin/mixash
An R package for adaptive shrinkage with mixture likelihood
  • * DESCRIPTION

Size: 13.7 KB - Last synced: over 1 year ago - Pushed: about 8 years ago

dcgerard/sabotash
A package that sabotages ASH.
  • * DESCRIPTION

Size: 33.2 KB - Last synced: over 1 year ago - Pushed: over 7 years ago

GabrielHoffman/dreamlet
Perform differential expression analysis on multi-sample single cell datasets using linear mixed models
  • * DESCRIPTION

Size: 231 MB - Last synced: 2 days ago - Pushed: 2 days ago

mildpiggy/DEP2
An r package for proteomics data Analysis, developed from DEP.
  • * DESCRIPTION

Size: 118 MB - Last synced: 3 days ago - Pushed: 3 days ago

nab-iak/DESeq2 Fork of mikelove/DESeq2
Differential gene expression analysis based on the negative binomial distribution
  • * DESCRIPTION

Size: 3.43 MB - Last synced: 11 months ago - Pushed: over 1 year ago

GenomicsNX/debrowser Fork of UMMS-Biocore/debrowser
Differential Count Data Analysis Toolbox
  • * DESCRIPTION

Size: 23.3 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago

felixshiyong/DESeq2 Fork of mikelove/DESeq2
Differential gene expression analysis based on the negative binomial distribution
  • * DESCRIPTION

Size: 3.02 MB - Last synced: 11 months ago - Pushed: over 5 years ago

zerack5/DESeq2 Fork of mikelove/DESeq2
Differential gene expression analysis based on the negative binomial distribution
  • * DESCRIPTION

Size: 3.4 MB - Last synced: 11 months ago - Pushed: almost 2 years ago

cran/MixTwice
:exclamation: This is a read-only mirror of the CRAN R package repository. MixTwice — Large-Scale Hypothesis Testing by Variance Mixing
  • * DESCRIPTION

Size: 5.08 MB - Last synced: 8 months ago - Pushed: over 2 years ago

bioc/DESeq2
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 3.42 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

bioc/debrowser
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 23.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

adamjdluo/RU_ATACseq Fork of RockefellerUniversity/RU_ATACseq
  • * atacseq/DESCRIPTION

Size: 154 MB - Last synced: 10 months ago - Pushed: almost 4 years ago

areyesq89/DESeq2 Fork of mikelove/DESeq2
Differential gene expression analysis based on the negative binomial distribution
  • * DESCRIPTION

Size: 3.5 MB - Last synced: 10 months ago - Pushed: over 1 year ago

bioc/DiffBind
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 77.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

HaniceSun/DESeq2 Fork of thelovelab/DESeq2
Differential gene expression analysis based on the negative binomial distribution
  • * DESCRIPTION

Size: 3.2 MB - Last synced: 9 months ago - Pushed: over 4 years ago

biospi/seaMass
Differential expression analysis for mass spectrometry proteomics and metabolomics
  • >= 2.2 DESCRIPTION

Size: 14.2 MB - Last synced: 8 months ago - Pushed: 10 months ago

dunstone-a/QTLExperiment
S4 classes for QTL summary statistics and metadata
  • * DESCRIPTION

Size: 406 KB - Last synced: 15 days ago - Pushed: 4 months ago

willwerscheid/ebnm Fork of stephenslab/ebnm
R package to fit Empirical Bayes Normal Means model.
  • * DESCRIPTION

Size: 6.88 MB - Last synced: 20 days ago - Pushed: 20 days ago

vishalbelsare/ebnm Fork of stephenslab/ebnm
R package to fit Empirical Bayes Normal Means model.
  • * DESCRIPTION

Size: 6.89 MB - Last synced: 5 days ago - Pushed: 5 days ago

bioc/BindingSiteFinder
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 9.64 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

bioc/topconfects
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 577 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

ninhtran02/zdirect
  • * DESCRIPTION

Size: 1.47 MB - Last synced: 6 months ago - Pushed: 6 months ago

kkdey/classtpx
An R package for Semi-supervised Topic models
  • * DESCRIPTION

Size: 128 MB - Last synced: 16 days ago - Pushed: almost 6 years ago

bioc/dar
This is a read-only mirror of the git repos at https://bioconductor.org
  • * DESCRIPTION

Size: 1.73 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

NYUAD-Core-Bioinformatics/Nasqar2
  • * debrowser-master/DESCRIPTION

Size: 21.6 MB - Last synced: about 2 months ago - Pushed: 2 months ago

kiddddd1218/DESeq2_py
  • * The love/DESeq2-master/DESeq2-master/DESCRIPTION

Size: 2.94 MB - Last synced: 2 months ago - Pushed: 2 months ago

zisanurrahman/mikelove_DESeq2
  • * DESCRIPTION

Size: 2.9 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

stephenslab/gbcd
R package for generalized binary covariance decomposition.
  • * DESCRIPTION

Size: 88 MB - Last synced: 27 days ago - Pushed: 27 days ago