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 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
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## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
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## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
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## other attached packages:
## [1] BiocStyle_2.25.0
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## loaded via a namespace (and not attached):
##  [1] bookdown_0.26       digest_0.6.29       R6_2.5.1           
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##  [7] stringi_1.7.6       rlang_1.0.2         cli_3.3.0          
## [10] jquerylib_0.1.4     bslib_0.3.1         rmarkdown_2.14     
## [13] tools_4.2.0         stringr_1.4.0       xfun_0.30          
## [16] yaml_2.3.5          fastmap_1.1.0       compiler_4.2.0     
## [19] BiocManager_1.30.17 htmltools_0.5.2     knitr_1.39         
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