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.sctk.science.

Session info

## R version 4.1.0 RC (2021-05-10 r80283)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_2.20.0
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.22       digest_0.6.27       R6_2.5.0           
##  [4] jsonlite_1.7.2      magrittr_2.0.1      evaluate_0.14      
##  [7] stringi_1.6.2       rlang_0.4.11        jquerylib_0.1.4    
## [10] bslib_0.2.5.1       rmarkdown_2.8       tools_4.1.0        
## [13] stringr_1.4.0       xfun_0.23           yaml_2.2.1         
## [16] compiler_4.1.0      BiocManager_1.30.15 htmltools_0.5.1.1  
## [19] knitr_1.33          sass_0.4.0