apeglm

This is the development version of apeglm; for the stable release version, see apeglm.

Approximate posterior estimation for GLM coefficients

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.31.0
In Bioconductor since	BioC 3.6 (R-3.4) (8 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, DeeDeeExperiment, DESeq2, extraChIPs, fishpond, terapadog, 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_1.31.0.tar.gz
Windows Binary (x86_64)	apeglm_1.31.0.zip
macOS Binary (x86_64)	apeglm_1.31.0.tgz
macOS Binary (arm64)	apeglm_1.31.0.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/
Package Downloads Report	Download Stats