transformGamPoi
This is the released version of transformGamPoi; for the devel version, see transformGamPoi.
Variance Stabilizing Transformation for Gamma-Poisson Models
Bioconductor version: Release (3.23)
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("transformGamPoi")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Normalization, Preprocessing, Regression, SingleCell, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 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 | scTypeEval |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | transformGamPoi_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | transformGamPoi_1.18.0.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 |