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glmGamPoi

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

Fit a Gamma-Poisson Generalized Linear Model

Bioconductor version: Development (3.18)

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>

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

Installation

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

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

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

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

Details

biocViews RNASeq, Regression, SingleCell, Software
Version 1.13.2
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
Linking To 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
System Requirements C++11
Enhances
URL https://github.com/const-ae/glmGamPoi
Bug Reports https://github.com/const-ae/glmGamPoi/issues
See More
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_1.13.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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