ReducedExperiment

This is the released version of ReducedExperiment; for the devel version, see ReducedExperiment.

Containers and tools for dimensionally-reduced -omics representations

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DOI: 10.18129/B9.bioc.ReducedExperiment

Bioconductor version: Release (3.22)

Provides SummarizedExperiment-like containers for storing and manipulating dimensionally-reduced assay data. The ReducedExperiment classes allow users to simultaneously manipulate their original dataset and their decomposed data, in addition to other method-specific outputs like feature loadings. Implements utilities and specialised classes for the application of stabilised independent component analysis (sICA) and weighted gene correlation network analysis (WGCNA).

Author: Jack Gisby [aut, cre] ORCID iD ORCID: 0000-0003-0511-8123 , Michael Barnes [aut] ORCID iD ORCID: 0000-0001-9097-7381

Maintainer: Jack Gisby <jackgisby at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("ReducedExperiment")

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("ReducedExperiment")

ReducedExperiment HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Network, Software

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License GPL (>= 3)

Depends R (>= 4.4.0), SummarizedExperiment, methods

Imports WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer, car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices, BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors

System Requirements

URL https://github.com/jackgisby/ReducedExperiment

Bug Reports https://github.com/jackgisby/ReducedExperiment/issues

Suggests knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle, airway

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ReducedExperiment_1.2.0.tar.gz

Windows Binary (x86_64) ReducedExperiment_1.2.0.zip (64-bit only)

macOS Binary (x86_64) ReducedExperiment_1.2.0.tgz

macOS Binary (arm64) ReducedExperiment_1.2.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/ReducedExperiment

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReducedExperiment

Bioc Package Browser https://code.bioconductor.org/browse/ReducedExperiment/

Package Short Url https://bioconductor.org/packages/ReducedExperiment/

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