Package: transformGamPoi 1.19.0

Constantin Ahlmann-Eltze

transformGamPoi: Variance Stabilizing Transformation for Gamma-Poisson Models

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).

Authors:Constantin Ahlmann-Eltze [aut, cre]

# Install 'transformGamPoi' in R:

install.packages('transformGamPoi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/const-ae/transformgampoi/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:transformGamPoi-1.19.0(bioc 3.24)transformGamPoi-1.18.0(bioc 3.23)

singlecell normalization preprocessing regression cpp

6.21 score 22 stars 37 scripts 4 exports 38 dependencies

Last updated from:65fe01422d. Checks:1 NOTE, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	296
linux-devel-arm64	OK	262
linux-devel-x86_64	OK	349
source / vignettes	OK	287
linux-release-arm64	OK	280
linux-release-x86_64	OK	308
macos-release-arm64	OK	243
macos-release-x86_64	OK	301
macos-oldrel-arm64	OK	144
macos-oldrel-x86_64	OK	237
windows-devel	OK	1102
windows-release	OK	1018
windows-oldrel	OK	882
wasm-release	OK	208

Exports:acosh_transform residual_transform shifted_log_transform transformGamPoi

Dependencies:abind assorthead beachmat Biobase BiocGenerics biocmake cli DelayedArray DelayedMatrixStats dir.expiry filelock generics GenomicRanges glmGamPoi glue h5mread HDF5Array IRanges lattice lifecycle Matrix MatrixGenerics matrixStats Rcpp RcppArmadillo rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray sparseMatrixStats SummarizedExperiment vctrs XVector

transformGamPoi Quickstart

Installation | Example | Delta method-based variance stabilizing transformations | Model residuals-based variance stabilizing transformations | Session Info

Rendered fromtransformGamPoi.Rmdusingknitr::rmarkdown

Last update: 2021-08-26
Started: 2021-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Delta method-based variance stabilizing transformation	acosh_transform shifted_log_transform
Residual-based Variance Stabilizing Transformation	residual_transform
Variance Stabilizing Transformation for Gamma Poisson Data	transformGamPoi