Introduction to singleCellTK

David Jenkins1,2, Tyler Faits1,2, Rui Hong1,2, Zhe Wang1,2, Salam Abdullatif1, Vidya Akapoor3, Shruthi Bandyadka1,2, Xinyun Cao3, Yusuke Koga1,2, Anastasia Leshchyk1,2, Irzam Sarfraz1, Yichen Wang1, W. Evan Johnson1,2 and Joshua D. Campbell1,2*

1The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
2Program in Bioinformatics, Boston University, Boston, MA
3Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA

*camp@bu.edu

Package

singleCellTK 2.2.0

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.

• Installation/Introduction

1.1 Interactive Analysis

• Uploading Data
• Data Summary and Filtering
• Visualization and Clustering
• Batch Correction
• Differential Expression
• Pathway Activity Analysis
• Sample Size

1.2 R Console Analysis

• Processing and Visualizing Data in the Single Cell Toolkit
• Aligning and Quantifying scRNA-Seq Data

Session info

## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## 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