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This is the development version of celda; for the stable release version, see celda.

CEllular Latent Dirichlet Allocation

Bioconductor version: Development (3.20)

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

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

Maintainer: Joshua Campbell <camp at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analysis of single-cell genomic data with celda HTML R Script
Estimate and remove cross-contamination from ambient RNA in single-cell data with DecontX HTML R Script
Reference Manual PDF


biocViews Bayesian, Clustering, DataImport, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software
Version 1.21.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License MIT + file LICENSE
Depends R (>= 4.0), SingleCellExperiment, Matrix
Imports plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater(>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize
System Requirements
Bug Reports
See More
Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData
Linking To Rcpp, RcppEigen
Depends On Me
Imports Me decontX, singleCellTK
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_1.21.0.tar.gz
Windows Binary
macOS Binary (x86_64) celda_1.21.0.tgz
macOS Binary (arm64) celda_1.21.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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