celda
CEllular Latent Dirichlet Allocation
Bioconductor version: Release (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("celda")):
Installation
To install this package, start R (version "4.4") 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")| 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Clustering, DataImport, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | celda_1.20.0.zip |
| macOS Binary (x86_64) | celda_1.20.0.tgz |
| macOS Binary (arm64) | celda_1.20.0.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 |