DOI: 10.18129/B9.bioc.celda    

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

CEllular Latent Dirichlet Allocation

Bioconductor version: Development (3.13)

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


biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.7.3
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, scater(>= 1.14.4), scran, SingleCellExperiment, dbscan, DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure, circlize
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
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_1.7.3.tar.gz
Windows Binary celda_1.7.3.zip
macOS 10.13 (High Sierra) celda_1.7.3.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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