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 (3.23)
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")):
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("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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | ReducedExperiment_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | ReducedExperiment_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | ReducedExperiment_1.4.0.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/ |
| Package Downloads Report | Download Stats |