corral

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see corral.

Correspondence Analysis for Single Cell Data


Bioconductor version: 3.13

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 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 "4.1") 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")
alignment with corralm HTML R Script
dim reduction with corral HTML R Script
Reference Manual PDF

Details

biocViews BatchEffect, DimensionReduction, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization
Version 1.2.0
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, SingleCellExperiment, SummarizedExperiment, transport
System Requirements
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Suggests ade4, BiocStyle, CellBench, DuoClustering2018, knitr, testthat
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Depends On Me OSCA.advanced
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Package Archives

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

Source Package corral_1.2.0.tar.gz
Windows Binary corral_1.2.0.zip
macOS 10.13 (High Sierra) corral_1.2.0.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
Old Source Packages for BioC 3.13 Source Archive