singleCellTK

DOI: 10.18129/B9.bioc.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>

Installation

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

if (!requireNamespace("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")

 

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, ImmunoOncology, SingleCell, Software
Version	1.4.2
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 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
LinkingTo
Suggests	testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase, lintr
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_1.4.2.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
Package Short Url	https://bioconductor.org/packages/singleCellTK/
Package Downloads Report	Download Stats