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Bioconductor - ReducedExperiment (development version)

ReducedExperiment

This is the development version of ReducedExperiment; for the stable release version, see ReducedExperiment.

Containers and tools for dimensionally-reduced -omics representations

Bioconductor version: Development (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: 0000-0003-0511-8123 , Michael Barnes [aut] 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Network, Software Version 1.1.2 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) 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 See More Package Archives

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

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