transformGamPoi

DOI: 10.18129/B9.bioc.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 (3.15)

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>

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

Installation

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

if (!requireNamespace("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")

 

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Details

biocViews Normalization, Preprocessing, Regression, SingleCell, Software
Version 1.1.2
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.1.2.tar.gz
Windows Binary
macOS 10.13 (High Sierra) transformGamPoi_1.1.2.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

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