transformGamPoi

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see transformGamPoi.

Variance Stabilizing Transformation for Gamma-Poisson Models

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Normalization, Preprocessing, Regression, SingleCell, Software

Version 1.10.0

In Bioconductor since BioC 3.14 (R-4.1) (3 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

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_1.10.0.tar.gz

Windows Binary (x86_64) transformGamPoi_1.10.0.zip

macOS Binary (x86_64) transformGamPoi_1.10.0.tgz

macOS Binary (arm64) transformGamPoi_1.10.0.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

Old Source Packages for BioC 3.19 Source Archive