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 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.30       digest_0.6.30       R6_2.5.1           
##  [4] lifecycle_1.0.3     jsonlite_1.8.3      magrittr_2.0.3     
##  [7] evaluate_0.18       stringi_1.7.8       cachem_1.0.6       
## [10] rlang_1.0.6         cli_3.4.1           jquerylib_0.1.4    
## [13] bslib_0.4.1         vctrs_0.5.1         rmarkdown_2.18     
## [16] tools_4.2.1         stringr_1.5.0       glue_1.6.2         
## [19] xfun_0.35           yaml_2.3.6          fastmap_1.1.0      
## [22] compiler_4.2.1      BiocManager_1.30.19 htmltools_0.5.3    
## [25] knitr_1.41          sass_0.4.4