# Introduction to singleCellTK

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.

# 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 4.5.2 (2025-10-31)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
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    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
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    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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    ## time zone: Etc/UTC
    ## tzcode source: system (glibc)
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    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
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    ## other attached packages:
    ## [1] BiocStyle_2.39.0
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    ## loaded via a namespace (and not attached):
    ##  [1] digest_0.6.39       R6_2.6.1            fastmap_1.2.0
    ##  [4] xfun_0.55           maketools_1.3.2     cachem_1.1.0
    ##  [7] knitr_1.51          htmltools_0.5.9     rmarkdown_2.30
    ## [10] buildtools_1.0.0    lifecycle_1.0.5     cli_3.6.5
    ## [13] sass_0.4.10         jquerylib_0.1.4     compiler_4.5.2
    ## [16] sys_3.4.3           tools_4.5.2         bslib_0.9.0
    ## [19] evaluate_1.0.5      yaml_2.3.12         otel_0.2.0
    ## [22] BiocManager_1.30.27 jsonlite_2.0.0      rlang_1.1.7