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transformGamPoi

This is the development version of transformGamPoi; for the stable release version, see transformGamPoi.

Variance Stabilizing Transformation for Gamma-Poisson Models

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL-3
Depends
Imports glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp
Linking To Rcpp
Suggests testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle
System Requirements
Enhances
URL https://github.com/const-ae/transformGamPoi
Bug Reports https://github.com/const-ae/transformGamPoi/issues
See More
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_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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