Package: singleCellTK Type: Package Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data Version: 2.23.0 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0003-4347-5199")), person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0001-8121-792X")), person(given="Rui", family="Hong", email="rzhong@bu.edu", role=c("aut")), person(given="Yusuke", family="Koga", email="ykoga07@bu.edu", role=c("aut")), person(given="Salam", family="Alabdullatif", email="salamha@bu.edu", role=c("aut")), person(given="Nida", family="Pervaiz", email="nidapervaiz27@gmail.com", role=c("aut")), person(given="David", family="Jenkins", email="dfj@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0002-7451-4288")), person(given="Vidya", family="Akavoor", email="vidyaap@bu.edu", role=c("aut")), person(given="Xinyun", family="Cao", email="xcao19@bu.edu", role=c("aut")), person(given="Shruthi", family="Bandyadka", email="sbandya@bu.edu", role=c("aut")), person(given="Anastasia", family="Leshchyk", email="aleshchk@bu.edu", role=c("aut")), person(given="Tyler", family="Faits", email="tfaits@bu.edu", role=c("aut")), person(given=c("Mohammed", "Muzamil"), family="Khan", email="mmkhan@bu.edu", role=c("aut")), person(given="Zhe", family="Wang", email="zhe@bu.edu", role=c("aut")), person(given=c("W.", "Evan"), family="Johnson", email="wej@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0002-6247-6595")), person(given="Ming", family="Liu", email="mingl@bu.edu", role=c("aut")), person(given=c("Joshua", "David"), family="Campbell", email="camp@bu.edu", role=c("aut", "cre"), comment = c(ORCID = "0000-0003-0780-8662")) ) Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Description: 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. License: MIT + file LICENSE Encoding: UTF-8 biocViews: SingleCell, GeneExpression, DifferentialExpression, Alignment, Clustering, ImmunoOncology, BatchEffect, Normalization, QualityControl, DataImport, GUI LazyData: FALSE 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, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, 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, lifecycle RoxygenNote: 7.3.3 Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse VignetteBuilder: knitr URL: https://www.camplab.net/sctk/ BugReports: https://github.com/compbiomed/singleCellTK/issues Language: en-US Config/pak/sysreqs: libcairo2-dev cmake libfftw3-dev libfontconfig1-dev libfreetype6-dev libglpk-dev make libmagick++-dev gsfonts libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl python3 libnode-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 13:03:00 UTC RemoteUrl: https://github.com/bioc/singleCellTK RemoteRef: HEAD RemoteSha: 3ac722fca9cb1a1ce3c09ce2fc13e2995c9535d1 NeedsCompilation: no Packaged: 2026-07-04 03:31:41 UTC; root Author: Yichen Wang [aut] (ORCID: ), Irzam Sarfraz [aut] (ORCID: ), Rui Hong [aut], Yusuke Koga [aut], Salam Alabdullatif [aut], Nida Pervaiz [aut], David Jenkins [aut] (ORCID: ), 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] (ORCID: ), Ming Liu [aut], Joshua David Campbell [aut, cre] (ORCID: ) Maintainer: Joshua David Campbell