celda

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see celda.

CEllular Latent Dirichlet Allocation


Bioconductor version: 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")):

Installation

To install this package, start R (version "4.1") 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 PDF R Script
Estimate and remove cross-contamination from ambient RNA in single-cell data with DecontX PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.8.1
In Bioconductor since BioC 3.9 (R-3.6) (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, 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
System Requirements
URL
Bug Reports https://github.com/campbio/celda/issues
See More
Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData, singleCellTK
Linking To Rcpp, RcppEigen
Enhances
Depends On Me
Imports Me 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_1.8.1.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
Bioc Package Browser https://code.bioconductor.org/browse/celda/
Package Short Url https://bioconductor.org/packages/celda/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive