singleCellTK

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: 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>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("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")

1. Introduction to singleCellTK HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software

Version 2.2.0

In Bioconductor since BioC 3.7 (R-3.5) (6 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

System Requirements

URL https://compbiomed.github.io/sctk_docs/

Bug Reports https://github.com/compbiomed/singleCellTK/issues

Suggests testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me celda

Links To Me

Build Report 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

Bioc Package Browser https://code.bioconductor.org/browse/singleCellTK/

Package Short Url https://bioconductor.org/packages/singleCellTK/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.13 Source Archive