singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK    

This is the development version of singleCellTK; to use it, please install the devel version of Bioconductor.

Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.5.8
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, shinyBS, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, shinythemes, umap
LinkingTo
Suggests testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase
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_1.5.8.tar.gz
Windows Binary singleCellTK_1.5.8.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) singleCellTK_1.5.8.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

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