glmGamPoi

This is the released version of glmGamPoi; for the devel version, see glmGamPoi.

Fit a Gamma-Poisson Generalized Linear Model

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.glmGamPoi

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-3762-068X , Nathan Lubock [ctb] ORCID iD ORCID: 0000-0001-8064-2465 , 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews RNASeq, Regression, SingleCell, Software

Version 1.22.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 years)

License GPL-3

Depends R (>= 4.1.0)

Imports Rcpp, beachmat, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray(>= 1.5.21), S4Vectors, DelayedArray, HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs

System Requirements C++17

URL https://github.com/const-ae/glmGamPoi

Bug Reports https://github.com/const-ae/glmGamPoi/issues

Suggests testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, dplyr

Linking To Rcpp, RcppArmadillo, beachmat, assorthead

Enhances

Depends On Me

Imports Me BASiCStan, lemur, transformGamPoi, SCdeconR

Suggests Me DESeq2, DEXSeq, Seurat

Links To Me

Build Report Build Report

Package Archives

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

Source Package glmGamPoi_1.22.0.tar.gz

Windows Binary (x86_64) glmGamPoi_1.21.0.zip (64-bit only)

macOS Binary (x86_64) glmGamPoi_1.22.0.tgz

macOS Binary (arm64) glmGamPoi_1.22.0.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