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glmGamPoi

Fit a Gamma-Poisson Generalized Linear Model

Bioconductor version: 3.24 · Package version: 1.25.1

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.

Installation

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

BiocManager::install("glmGamPoi")

Details

MaintainerConstantin Ahlmann-Eltze <artjom31415@googlemail.com>
AuthorConstantin Ahlmann-Eltze [aut, cre] (ORCID: <https://orcid.org/0000-0002-3762-068X>), Nathan Lubock [ctb] (ORCID: <https://orcid.org/0000-0001-8064-2465>), Michael Love [ctb]
LicenseMIT + file LICENSE
URLhttps://github.com/const-ae/glmGamPoi
Bug Reportshttps://github.com/const-ae/glmGamPoi/issues
System RequirementsC++17
Downloads rank6780
Source branchdevel
biocViewsRNASeq, Regression, SingleCell, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageglmGamPoi_1.25.1.tar.gz
Windows binary (x86_64)glmGamPoi_1.25.1.zip
macOS binary (arm64)glmGamPoi_1.25.1.tgz
macOS binary (x86_64)glmGamPoi_1.25.1.tgz
Dependencies

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

LinkingTo: Rcpp, RcppArmadillo, beachmat, assorthead

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

Reverse dependencies

Imports Me (4): BASiCStan, DOtools, lemur, transformGamPoi

Suggests Me (7): DESeq2, DEXSeq, fishash, scregclust, scTypeEval, Seurat, singIST