apeglm

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see apeglm.

Approximate posterior estimation for GLM coefficients

Bioconductor version: 3.20

apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.

Author: Anqi Zhu [aut, cre], Joshua Zitovsky [ctb], Joseph Ibrahim [aut], Michael Love [aut]

Maintainer: Anqi Zhu <anqizhu at live.unc.edu>

Citation (from within R, enter citation("apeglm")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("apeglm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("apeglm")

Effect size estimation with apeglm HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software

Version 1.28.0

In Bioconductor since BioC 3.6 (R-3.4) (7.5 years)

License GPL-2

Depends

Imports emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp

System Requirements

URL

Suggests DESeq2, airway, knitr, rmarkdown, testthat

Linking To Rcpp, RcppEigen, RcppNumerical

Enhances

Depends On Me rnaseqGene

Imports Me airpart, debrowser, DiffBind, ERSSA, phantasus, Rmmquant, TEKRABber

Suggests Me bambu, dar, DESeq2, extraChIPs, fishpond, NanoporeRNASeq, RNAseqQC

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package apeglm_1.28.0.tar.gz

Windows Binary (x86_64) apeglm_1.28.0.zip

macOS Binary (x86_64) apeglm_1.28.0.tgz

macOS Binary (arm64) apeglm_1.28.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/apeglm

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/apeglm

Bioc Package Browser https://code.bioconductor.org/browse/apeglm/

Package Short Url https://bioconductor.org/packages/apeglm/

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