apeglm

DOI: 10.18129/B9.bioc.apeglm    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see apeglm.

Approximate posterior estimation for GLM coefficients

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Effect size estimation with apeglm
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	GPL-2
Depends
Imports	emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp
LinkingTo	Rcpp, RcppEigen, RcppNumerical
Suggests	DESeq2, airway, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me	rnaseqGene
Imports Me	airpart, debrowser, DiffBind, exomePeak2
Suggests Me	bambu, BRGenomics, DESeq2, fishpond, NanoporeRNASeq
Links To Me
Build Report

Package Archives

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

Source Package	apeglm_1.14.0.tar.gz
Windows Binary	apeglm_1.14.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	apeglm_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/apeglm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/apeglm
Package Short Url	https://bioconductor.org/packages/apeglm/
Package Downloads Report	Download Stats