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glmGamPoi

Fit a Gamma-Poisson Generalized Linear Model


Bioconductor version: Release (3.19)

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] , Nathan Lubock [ctb] , 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 "4.4") 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")
glmGamPoi Quickstart HTML R Script
Pseudobulk and differential expression HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews RNASeq, Regression, SingleCell, Software
Version 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends
Imports Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs
System Requirements C++11
URL https://github.com/const-ae/glmGamPoi
Bug Reports https://github.com/const-ae/glmGamPoi/issues
See More
Suggests testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr
Linking To Rcpp, RcppArmadillo, beachmat
Enhances
Depends On Me
Imports Me BASiCStan, lemur, transformGamPoi, SCdeconR
Suggests Me DESeq2, DEXSeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package glmGamPoi_1.16.0.tar.gz
Windows Binary glmGamPoi_1.16.0.zip
macOS Binary (x86_64) glmGamPoi_1.16.0.tgz
macOS Binary (arm64) glmGamPoi_1.16.0.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