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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
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
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
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