transformGamPoi

DOI: 10.18129/B9.bioc.transformGamPoi    

Variance Stabilizing Transformation for Gamma-Poisson Models

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	glmGamPoi Quickstart
PDF		Reference Manual
Text		NEWS

Details

biocViews	Normalization, Preprocessing, Regression, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-3
Depends
Imports	glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp
LinkingTo	Rcpp
Suggests	testthat, TENxPBMCData, scran, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/const-ae/transformGamPoi
BugReports	https://github.com/const-ae/transformGamPoi/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	transformGamPoi_1.2.0.tar.gz
Windows Binary	transformGamPoi_1.2.0.zip
macOS Binary (x86_64)	transformGamPoi_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/transformGamPoi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/transformGamPoi
Package Short Url	https://bioconductor.org/packages/transformGamPoi/
Package Downloads Report	Download Stats