DOI: 10.18129/B9.bioc.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>

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


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HTML R Script 1. Introduction to singleCellTK
PDF   Reference Manual
Text   NEWS


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
Suggests testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling,, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics
Depends On Me
Imports Me
Suggests Me celda
Links To Me
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