corral

DOI: 10.18129/B9.bioc.corral  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see corral.

Correspondence Analysis for Single Cell Data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	BatchEffect, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	GPL-2
Depends
Imports	ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport
LinkingTo
Suggests	ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat
SystemRequirements
Enhances
URL
Depends On Me	OSCA.advanced
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	corral_1.10.0.tar.gz
Windows Binary	corral_1.10.0.zip
macOS Binary (x86_64)	corral_1.10.0.tgz
macOS Binary (arm64)	corral_1.10.0.tgz
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