singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK    

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Release (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")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("singleCellTK", version = "3.8")

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, SingleCell, Software
Version 1.2.2
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
LinkingTo
Suggests testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling
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_1.2.2.tar.gz
Windows Binary singleCellTK_1.2.2.zip
Mac OS X 10.11 (El Capitan) singleCellTK_1.2.2.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 http://bioconductor.org/packages/singleCellTK/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: