celda

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see celda.

CEllular Latent Dirichlet Allocation

Bioconductor version: 3.9

celda leverages Bayesian hierarchical modeling to cluster genes, cells, or both simultaneously from single cell sequencing data.

Author: Joshua Campbell [aut, cre], Sean Corbett [aut], Yusuke Koga [aut], Zhe Wang [aut]

Maintainer: Joshua Campbell <camp at bu.edu>

Citation (from within R, enter citation("celda")):

Installation

To install this package, start R (version "3.6") and enter:


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

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("celda")

Analyzing single-cell RNA-seq count data with celda HTML R Script

Estimate and remove cross-contamination from ambient RNA for scRNA-seq data with DecontX HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software

Version 1.0.4

In Bioconductor since BioC 3.9 (R-3.6) (5 years)

License MIT + file LICENSE

Depends R (>= 3.6)

Imports stats, plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, gridExtra, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, umap, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr

System Requirements

URL

Bug Reports https://github.com/campbio/celda/issues

Suggests testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle

Linking To Rcpp, RcppEigen

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 celda_1.0.4.tar.gz

Windows Binary celda_1.0.4.zip

Mac OS X 10.11 (El Capitan) celda_1.0.4.tgz

Source Repository git clone https://git.bioconductor.org/packages/celda

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/celda

Bioc Package Browser https://code.bioconductor.org/browse/celda/

Package Short Url https://bioconductor.org/packages/celda/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.9 Source Archive