DOI: 10.18129/B9.bioc.celda    

CEllular Latent Dirichlet Allocation

Bioconductor version: Release (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>

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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 1.8.1
In Bioconductor since BioC 3.9 (R-3.6) (2 years)
License MIT + file LICENSE
Depends R (>= 4.0)
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, SingleCellExperiment, dbscan, DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure, circlize
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData, singleCellTK
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_1.8.1.tar.gz
Windows Binary celda_1.8.1.zip
macOS 10.13 (High Sierra) celda_1.8.1.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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