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 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
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## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## locale:
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
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## other attached packages:
## [1] BiocStyle_2.33.0
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## loaded via a namespace (and not attached):
##  [1] digest_0.6.35       R6_2.5.1            bookdown_0.39      
##  [4] fastmap_1.1.1       xfun_0.43           cachem_1.0.8       
##  [7] knitr_1.46          htmltools_0.5.8.1   rmarkdown_2.26     
## [10] lifecycle_1.0.4     cli_3.6.2           sass_0.4.9         
## [13] jquerylib_0.1.4     compiler_4.4.0      tools_4.4.0        
## [16] evaluate_0.23       bslib_0.7.0         yaml_2.3.8         
## [19] BiocManager_1.30.22 jsonlite_1.8.8      rlang_1.1.3