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Bioconductor - celda

celda

This is the released version of celda; for the devel version, see celda.

CEllular Latent Dirichlet Allocation

Bioconductor version: Release (3.21)

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 bu.edu>

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

To install this package, start R (version "4.5") and enter:


if (!require("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")

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 NEWS Text LICENSE Text Details biocViews Bayesian, Clustering, DataImport, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software Version 1.24.0 In Bioconductor since BioC 3.9 (R-3.6) (6 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, dendextend, ggdendro, pROC System Requirements URL Bug Reports https://github.com/campbio/celda/issues See More Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData Linking To Rcpp, RcppEigen Enhances 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.

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