corral
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see corral.
Correspondence Analysis for Single Cell Data
Bioconductor version: 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("corral")):
Installation
To install this package, start R (version "4.0") 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 |
Details
| biocViews | BatchEffect, DimensionReduction, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization |
| Version | 1.0.0 |
| 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 | |
| URL |
See More
| Suggests | ade4, BiocStyle, CellBench, DuoClustering2018, knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.12 | Source Archive |