# Introduction to singleCellTK

Yichen Wang1, Irzam Sarfraz1, Rui Hong1,2, Yusuke Koga1,2, Salam Abdullatif1, Nida Pervaiz1, David Jenkins1,2, Vidya Akavoor3, Xinyun Cao3, Shruthi Bandyadka1,2, Anastasia Leshchyk1,2, Tyler Faits1,2, Mohammed Muzamil Khan1,2, Zhe Wang1,2, W. Evan Johnson1,2, Ming Liu1,2 and Joshua D. Campbell1,2*

1The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
2Program in Bioinformatics, Boston University, Boston, MA
3Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA

*camp@bu.edu

#### 3 July 2025

#### Package

singleCellTK 2.18.1

# Contents

The Single Cell Toolkit (SCTK) is an interactive scRNA-Seq analysis package that allows a user to upload raw scRNA-Seq count matrices and perform downstream scRNA-Seq analysis interactively through a web interface, or through a set of R functions through the command line. The package is written in R with a graphical user interface (GUI) written in Shiny. Users can perform analysis with modules for conducting quality control, clustering, batch correction, differential expression, pathway enrichment, and sample size calculator, all in a simple to use point and click interface. The toolkit also supports command line data processing, and results can be loaded into the GUI for additional exploration and downstream analysis.

# 1 Vignettes

Due to the range of features that are available in SCTK, we have prepared several vignettes to help you get started, which are all available at https://www.camplab.net/sctk/

# Session info

    ## R version 4.5.1 (2025-06-13 ucrt)
    ## Platform: x86_64-w64-mingw32/x64
    ## Running under: Windows Server 2022 x64 (build 20348)
    ##
    ## Matrix products: default
    ##   LAPACK version 3.12.1
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=English_United States.utf8
    ## [3] LC_MONETARY=English_United States.utf8
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=English_United States.utf8
    ##
    ## time zone: America/New_York
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] BiocStyle_2.36.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] digest_0.6.37       R6_2.6.1            bookdown_0.43
    ##  [4] fastmap_1.2.0       xfun_0.52           cachem_1.1.0
    ##  [7] knitr_1.50          htmltools_0.5.8.1   rmarkdown_2.29
    ## [10] lifecycle_1.0.4     cli_3.6.5           sass_0.4.10
    ## [13] jquerylib_0.1.4     compiler_4.5.1      tools_4.5.1
    ## [16] evaluate_1.0.4      bslib_0.9.0         yaml_2.3.10
    ## [19] BiocManager_1.30.26 jsonlite_2.0.0      rlang_1.1.6