DOI: 10.18129/B9.bioc.singleCellTK    

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

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Development (3.9)

Run common single cell analysis directly through your browser including differential expression, downsampling analysis, and clustering.

Author: David Jenkins

Maintainer: David Jenkins <dfj at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("singleCellTK", version = "3.9")

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
HTML R Script 2. Processing and Visualizing Data in the Single Cell Toolkit
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software
Version 1.3.7
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License MIT + file LICENSE
Depends R (>= 3.5), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase
Imports ape, colourpicker, cluster, ComplexHeatmap, data.table, DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly, RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, shinycssloaders, shinythemes, umap
Suggests testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown,,, scRNAseq, xtable, spelling, GSEABase
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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Follow Installation instructions to use this package in your R session.

Source Package singleCellTK_1.3.7.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) singleCellTK_1.3.7.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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