glmGamPoi

DOI: 10.18129/B9.bioc.glmGamPoi  

Fit a Gamma-Poisson Generalized Linear Model

Bioconductor version: Release (3.17)

Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

Author: Constantin Ahlmann-Eltze [aut, cre] , Michael Love [ctb]

Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("glmGamPoi")

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("glmGamPoi")

 

HTML	R Script	glmGamPoi Quickstart
HTML	R Script	Pseudobulk and differential expression
PDF		Reference Manual
Text		NEWS

Details

biocViews	RNASeq, Regression, SingleCell, Software
Version	1.12.2
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL-3
Depends
Imports	Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs
LinkingTo	Rcpp, RcppArmadillo, beachmat
Suggests	testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr
SystemRequirements	C++11
Enhances
URL	https://github.com/const-ae/glmGamPoi
BugReports	https://github.com/const-ae/glmGamPoi/issues
Depends On Me
Imports Me	BASiCStan, transformGamPoi
Suggests Me	DESeq2
Links To Me
Build Report

Package Archives

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

Source Package	glmGamPoi_1.12.2.tar.gz
Windows Binary	glmGamPoi_1.11.7.zip
macOS Binary (x86_64)	glmGamPoi_1.12.2.tgz
macOS Binary (arm64)	glmGamPoi_1.12.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/glmGamPoi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/glmGamPoi
Bioc Package Browser	https://code.bioconductor.org/browse/glmGamPoi/
Package Short Url	https://bioconductor.org/packages/glmGamPoi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive