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celda

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

CEllular Latent Dirichlet Allocation


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.1
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
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.

Source Package celda_1.19.1.tar.gz
Windows Binary celda_1.19.1.zip
macOS Binary (x86_64) celda_1.19.1.tgz
macOS Binary (arm64) celda_1.19.1.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