transformGamPoi
Variance Stabilizing Transformation for Gamma-Poisson Models
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("transformGamPoi")Details
| Maintainer | Constantin Ahlmann-Eltze <artjom31415@googlemail.com> |
| Author | Constantin Ahlmann-Eltze [aut, cre] (ORCID: <https://orcid.org/0000-0002-3762-068X>) |
| License | GPL-3 |
| URL | https://github.com/const-ae/transformGamPoi |
| Bug Reports | https://github.com/const-ae/transformGamPoi/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Normalization, Preprocessing, Regression, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/transformGamPoi/ |
Citation
From within R, enter citation("transformGamPoi"):
Constantin Ahlmann-Eltze. transformGamPoi: Variance Stabilizing Transformation for Gamma-Poisson Models. doi:10.18129/B9.bioc.transformGamPoi, R package version 1.18.0, https://bioconductor.org/packages/transformGamPoi.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | transformGamPoi_1.18.0.tar.gz |
| Windows binary (x86_64) | transformGamPoi_1.18.0.zip |
| macOS binary (arm64) | transformGamPoi_1.18.0.tgz |
| macOS binary (x86_64) | transformGamPoi_1.18.0.tgz |
Dependencies
Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp
LinkingTo: Rcpp
Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle
Reverse dependencies
Suggests Me (1): scTypeEval