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apeglm

Approximate posterior estimation for GLM coefficients


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Bayesian, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-2
Depends
Imports emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp
System Requirements
URL
See More
Suggests DESeq2, airway, knitr, rmarkdown, testthat
Linking To Rcpp, RcppEigen, RcppNumerical
Enhances
Depends On Me rnaseqGene
Imports Me airpart, debrowser, DiffBind, ERSSA, Rmmquant, TEKRABber
Suggests Me bambu, BRGenomics, DESeq2, fishpond, NanoporeRNASeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package apeglm_1.24.0.tar.gz
Windows Binary apeglm_1.24.0.zip (64-bit only)
macOS Binary (x86_64) apeglm_1.24.0.tgz
macOS Binary (arm64) apeglm_1.24.0.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