corral

DOI: 10.18129/B9.bioc.corral    

Correspondence Analysis for Single Cell Data

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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

Details

biocViews BatchEffect, DimensionReduction, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-2
Depends
Imports ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, SingleCellExperiment, SummarizedExperiment, transport
LinkingTo
Suggests ade4, BiocStyle, CellBench, DuoClustering2018, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
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_1.0.0.tar.gz
Windows Binary corral_1.0.0.zip
macOS 10.13 (High Sierra) corral_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/corral
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/corral
Package Short Url https://bioconductor.org/packages/corral/
Package Downloads Report Download Stats

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