celda

DOI: 10.18129/B9.bioc.celda    

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

CEllular Latent Dirichlet Allocation

Bioconductor version: Development (3.12)

Utilizing Bayesian hierarchical models to analyze single-cell genomic 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 "4.0") 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")

 

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
Text   LICENSE

Details

biocViews Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software
Version 1.5.12
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, scater(>= 1.14.4), scran, SingleCellExperiment, dbscan, DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure, circlize
LinkingTo Rcpp, RcppEigen
Suggests testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
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_1.5.12.tar.gz
Windows Binary celda_1.5.12.zip
macOS 10.13 (High Sierra) celda_1.5.12.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/
Package Downloads Report Download Stats

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