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corral

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

Correspondence Analysis for Single Cell Data


Bioconductor version: Development (3.19)

Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.

Author: Lauren Hsu [aut, cre] , Aedin Culhane [aut]

Maintainer: Lauren Hsu <lrnshoe at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("corral")

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("corral")
alignment with corralm HTML R Script
dim reduction with corral HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-2
Depends
Imports ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport
System Requirements
URL
See More
Suggests ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat
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Package Archives

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

Source Package corral_1.13.0.tar.gz
Windows Binary corral_1.13.0.zip (64-bit only)
macOS Binary (x86_64) corral_1.13.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/corral
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/corral
Bioc Package Browser https://code.bioconductor.org/browse/corral/
Package Short Url https://bioconductor.org/packages/corral/
Package Downloads Report Download Stats