celda
This is thereleased version of celda; for the devel version, seecelda.
CEllular Latent Dirichlet Allocation
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("celda")For older versions of R, please refer to the appropriateBioconductor 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 | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 years) |
| License | MIT + fileLICENSE |
| 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,dendextend,ggdendro,pROC |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | celda_1.26.0.tar.gz |
| Windows Binary (x86_64) | celda_1.26.0.zip |
| macOS Binary (x86_64) | celda_1.26.0.tgz |
| macOS Binary (arm64) | celda_1.26.0.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 |