DOI: 10.18129/B9.bioc.celda    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see celda.

CEllular Latent Dirichlet Allocation

Bioconductor version: 3.10

celda is a Bayesian hierarchical model that can co-cluster features and cells in single cell sequencing data.

Author: Joshua Campbell [aut, cre], Sean Corbett [aut], Yusuke Koga [aut], Shiyi Yang [aut], Eric Reed [aut], Zhe Wang [aut]

Maintainer: Joshua Campbell <camp at bu.edu>

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


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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
HTML R Script Sorting and annotation of single-cell clustering results with multiclass decision trees
PDF   Reference Manual
Text   NEWS


biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.2.4
In Bioconductor since BioC 3.9 (R-3.6) (1 year)
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, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, magrittr
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle
BugReports https://github.com/campbio/celda/issues
Depends On Me
Imports Me singleCellTK
Suggests Me
Links To Me
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Source Package celda_1.2.4.tar.gz
Windows Binary celda_1.2.4.zip
Mac OS X 10.11 (El Capitan) celda_1.2.4.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/
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