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transformGamPoi

Variance Stabilizing Transformation for Gamma-Poisson Models


Bioconductor version: Release (3.18)

Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., 'acosh', 'log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).

Author: Constantin Ahlmann-Eltze [aut, cre]

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

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

Installation

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


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

BiocManager::install("transformGamPoi")

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("transformGamPoi")
glmGamPoi Quickstart HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Normalization, Preprocessing, Regression, SingleCell, Software
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends
Imports glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp
System Requirements
URL https://github.com/const-ae/transformGamPoi
Bug Reports https://github.com/const-ae/transformGamPoi/issues
See More
Suggests testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package transformGamPoi_1.8.0.tar.gz
Windows Binary transformGamPoi_1.8.0.zip
macOS Binary (x86_64)
macOS Binary (arm64) transformGamPoi_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/transformGamPoi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/transformGamPoi
Bioc Package Browser https://code.bioconductor.org/browse/transformGamPoi/
Package Short Url https://bioconductor.org/packages/transformGamPoi/
Package Downloads Report Download Stats