singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK    

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Release (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>

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

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

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 1.0.2
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
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
Build Report  

Package Archives

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

Source Package singleCellTK_1.0.2.tar.gz
Windows Binary singleCellTK_1.0.2.zip
Mac OS X 10.11 (El Capitan) singleCellTK_1.0.2.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 3.7 Source Archive

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