celda

DOI: 10.18129/B9.bioc.celda    

CEllular Latent Dirichlet Allocation

Bioconductor version: Release (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 (!requireNamespace("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")

 

HTML R Script 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
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.0.4
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle
SystemRequirements
Enhances
URL
BugReports https://github.com/campbio/celda/issues
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 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
Package Short Url https://bioconductor.org/packages/celda/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive

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