singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK    

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Release (3.13)

Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..

Author: David Jenkins [aut] , Vidya Akavoor [aut], Salam Alabdullatif [aut], Shruthi Bandyadka [aut], Emma Briars [aut] , Xinyun Cao [aut], Sebastian Carrasco Pro [aut], Tyler Faits [aut], Rui Hong [aut], Mohammed Muzamil Khan [aut], Yusuke Koga [aut, cre], Anastasia Leshchyk [aut], Irzam Sarfraz [aut], Yichen Wang [aut], Zhe Wang [aut], W. Evan Johnson [aut] , Joshua David Campbell [aut]

Maintainer: Yusuke Koga <ykoga07 at bu.edu>

Installation

To install this package, start R (version "4.1") 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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software
Version	2.2.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase
Imports	ape, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer, ROCR, Rtsne, S4Vectors, scater, scMerge(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, uwot, DropletUtils, scds(>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq(>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap
LinkingTo
Suggests	testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics
SystemRequirements
Enhances
URL	https://compbiomed.github.io/sctk_docs/
BugReports	https://github.com/compbiomed/singleCellTK/issues
Depends On Me
Imports Me
Suggests Me	celda
Links To Me
Build Report

Package Archives

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

Source Package	singleCellTK_2.2.0.tar.gz
Windows Binary	singleCellTK_2.2.0.zip
macOS 10.13 (High Sierra)	singleCellTK_2.2.0.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