singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: 3.7

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("singleCellTK")

Documentation

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

browseVignettes("singleCellTK")

 

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
Text		LICENSE

Details

biocViews	Alignment, Clustering, DifferentialExpression, GeneExpression, SingleCell, Software
Version	1.0.3
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
LinkingTo
Suggests	testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable
SystemRequirements
Enhances
URL	https://compbiomed.github.io/sctk_docs/
BugReports	https://github.com/compbiomed/singleCellTK/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	singleCellTK_1.0.3.tar.gz
Windows Binary	singleCellTK_1.0.3.zip
Mac OS X 10.11 (El Capitan)	singleCellTK_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/singleCellTK
Source Repository (Developer Access)	git clone [email protected]:packages/singleCellTK
Package Short Url	http://bioconductor.org/packages/singleCellTK/
Package Downloads Report	Download Stats