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singleCellTK

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.

Interactive Analysis of Single Cell RNA-Seq Data


Bioconductor version: 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 bu.edu>

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

Installation

To install this package, start R (version "3.6") 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.

Documentation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software
Version 1.4.2
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
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
System Requirements
URL https://compbiomed.github.io/sctk_docs/
Bug Reports https://github.com/compbiomed/singleCellTK/issues
See More
Suggests testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase, lintr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package singleCellTK_1.4.2.tar.gz
Windows Binary singleCellTK_1.4.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) singleCellTK_1.4.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/singleCellTK
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/singleCellTK
Bioc Package Browser https://code.bioconductor.org/browse/singleCellTK/
Package Short Url https://bioconductor.org/packages/singleCellTK/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive