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 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-apple-darwin20
## Running under: macOS Monterey 12.7.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## 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_3.6.4           sass_0.4.10        
## [13] jquerylib_0.1.4     compiler_4.5.0      tools_4.5.0        
## [16] evaluate_1.0.3      bslib_0.9.0         yaml_2.3.10        
## [19] BiocManager_1.30.25 jsonlite_2.0.0      rlang_1.1.6