celda
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see celda.
CEllular Latent Dirichlet Allocation
Bioconductor version: 3.9
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], Zhe Wang [aut]
Maintainer: Joshua Campbell <camp at bu.edu>
citation("celda")):
Installation
To install this package, start R (version "3.6") 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")| 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 |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software |
| Version | 1.0.4 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/campbio/celda/issues |
See More
| Suggests | testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.0.4.tar.gz |
| Windows Binary | celda_1.0.4.zip |
| Mac OS X 10.11 (El Capitan) | celda_1.0.4.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 3.9 | Source Archive |