DOI: 10.18129/B9.bioc.singleCellTK    

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

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Development (3.14)

Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..

Author: Yichen Wang [aut, cre] , Irzam Sarfraz [aut], Rui Hong [aut], Yusuke Koga [aut], Salam Alabdullatif [aut], David Jenkins [aut] , Vidya Akavoor [aut], Xinyun Cao [aut], Shruthi Bandyadka [aut], Anastasia Leshchyk [aut], Tyler Faits [aut], Mohammed Muzamil Khan [aut], Zhe Wang [aut], W. Evan Johnson [aut] , Joshua David Campbell [aut]

Maintainer: Yichen Wang <wangych at>

Citation (from within R, enter citation("singleCellTK")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script 1. Introduction to singleCellTK
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software
Version 2.3.1
In Bioconductor since BioC 3.7 (R-3.5) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase
Imports ape, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer, ROCR, Rtsne, S4Vectors, scater, scMerge(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, DropletUtils, scds(>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq(>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, stats
Suggests testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling,, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics
Depends On Me
Imports Me
Suggests Me celda
Links To Me
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