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singleCellTK

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data


Bioconductor version: Release (3.18)

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] , Irzam Sarfraz [aut] , Rui Hong [aut], Yusuke Koga [aut], Salam Alabdullatif [aut], Nida Pervaiz [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] , Ming Liu [aut], Joshua David Campbell [aut, cre]

Maintainer: Joshua David Campbell <camp at bu.edu>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews Alignment, BatchEffect, Clustering, DataImport, DifferentialExpression, GUI, GeneExpression, ImmunoOncology, Normalization, QualityControl, SingleCell, Software
Version 2.12.2
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, anndata, 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 (>= 1.5-3), 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 (>= 3.2), celda, shinycssloaders, DropletUtils, scds(>= 1.2.0), reticulate (>= 1.14), tools, tximport, eds, 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, zellkonverter
System Requirements
URL https://www.camplab.net/sctk/
Bug Reports https://github.com/compbiomed/singleCellTK/issues
See More
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, SeuratObject, optparse
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_2.12.2.tar.gz
Windows Binary singleCellTK_2.12.2.zip
macOS Binary (x86_64) singleCellTK_2.12.2.tgz
macOS Binary (arm64)
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 3.18 Source Archive