celda

DOI: 10.18129/B9.bioc.celda    

This is the development version of celda; to use it, please install the devel version of Bioconductor.

CEllular Latent Dirichlet Allocation

Bioconductor version: Development (3.10)

celda leverages Bayesian hierarchical modeling to cluster genes, cells, or both simultaneously from single cell sequencing data.

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script Analyzing single-cell RNA-seq count data with celda
HTML R Script Estimate and remove cross-contamination from ambient RNA for scRNA-seq data with DecontX
HTML R Script Sorting and annotation of single-cell clustering results with multiclass decision trees
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.1.6
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports stats, plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, gridExtra, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, umap, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, magrittr
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle
SystemRequirements
Enhances
URL
BugReports https://github.com/campbio/celda/issues
Depends On Me
Imports Me singleCellTK
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package celda_1.1.6.tar.gz
Windows Binary celda_1.1.6.zip
Mac OS X 10.11 (El Capitan) celda_1.1.6.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 http://bioconductor.org/packages/celda/
Package Downloads Report Download Stats

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