singleCellTK

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: 3.8

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

Author: David Jenkins

Maintainer: David Jenkins <dfj at bu.edu>

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

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("singleCellTK")

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:

browseVignettes("singleCellTK")

1. Introduction to singleCellTK HTML R Script

2. Processing and Visualizing Data in the Single Cell Toolkit HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Version 1.2.3

In Bioconductor since BioC 3.7 (R-3.5) (6 years)

License MIT + file LICENSE

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

System Requirements

Suggests testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling

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