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 (3.21)
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] (ORCID:
Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>
citation("transformGamPoi")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Normalization, Preprocessing, Regression, SingleCell, Software |
| Version | 1.13.0 |
| 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 |
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_1.13.0.tar.gz |
| Windows Binary (x86_64) | transformGamPoi_1.13.0.zip |
| macOS Binary (x86_64) | transformGamPoi_1.13.0.tgz |
| macOS Binary (arm64) | transformGamPoi_1.13.0.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 |