celda
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see celda.
CEllular Latent Dirichlet Allocation
Bioconductor version: 3.10
celda is a Bayesian hierarchical model that can co-cluster features and cells in 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("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 |
Sorting and annotation of single-cell clustering results with multiclass decision trees | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Bayesian, Clustering, GeneExpression, Sequencing, SingleCell, Software |
Version | 1.2.4 |
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, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, magrittr |
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 | 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_1.2.4.tar.gz |
Windows Binary | celda_1.2.4.zip |
Mac OS X 10.11 (El Capitan) | celda_1.2.4.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/celda |
Source Repository (Developer Access) | git clone [email protected]: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 3.10 | Source Archive |