singleCellTK

DOI: 10.18129/B9.bioc.singleCellTK  

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Bioconductor version: Release (3.16)

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

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

Maintainer: Yichen Wang <wangych at bu.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Alignment, BatchEffect, Clustering, DataImport, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Normalization, QualityControl, SingleCell, Software
Version	2.8.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase
Imports	ape, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, SoupX, sva, reshape2, shinyalert, circlize, enrichR, celda, shinycssloaders, 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, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats
LinkingTo
Suggests	testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony
SystemRequirements
Enhances
URL	https://www.camplab.net/sctk/
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_2.8.0.tar.gz
Windows Binary	singleCellTK_2.8.0.zip
macOS Binary (x86_64)	singleCellTK_2.8.0.tgz
macOS Binary (arm64)	singleCellTK_2.8.0.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