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, ImmunoOncology, SingleCell, Software
Version 1.2.3
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, 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_1.2.3.tar.gz
Windows Binary singleCellTK_1.2.3.zip
Mac OS X 10.11 (El Capitan) singleCellTK_1.2.3.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

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