corral
Correspondence Analysis for Single Cell Data
Bioconductor version: Release (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>
citation("corral")):
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")| alignment with corralm | HTML | R Script |
| dim reduction with corral | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Linking To | |
| Suggests | ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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 |