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 4.3.2 Patched (2023-11-01 r85457)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## 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_2.30.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.34       R6_2.5.1            bookdown_0.37      
##  [4] fastmap_1.1.1       xfun_0.41           cachem_1.0.8       
##  [7] knitr_1.45          htmltools_0.5.7     rmarkdown_2.25     
## [10] lifecycle_1.0.4     cli_3.6.2           sass_0.4.8         
## [13] jquerylib_0.1.4     compiler_4.3.2      tools_4.3.2        
## [16] evaluate_0.23       bslib_0.6.1         yaml_2.3.8         
## [19] BiocManager_1.30.22 jsonlite_1.8.8      rlang_1.1.3