ReducedExperiment
This is the released version of ReducedExperiment; for the devel version, see ReducedExperiment.
Containers and tools for dimensionally-reduced -omics representations
Bioconductor version: Release (3.21)
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]
, Michael Barnes [aut]
Maintainer: Jack Gisby <jackgisby at gmail.com>
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 | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Network, Software |
| Version | 1.0.2 |
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle, airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ReducedExperiment_1.0.2.tar.gz |
| Windows Binary (x86_64) | ReducedExperiment_1.0.2.zip |
| macOS Binary (x86_64) | ReducedExperiment_1.0.2.tgz |
| macOS Binary (arm64) | ReducedExperiment_1.0.2.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.21 | Source Archive |