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bioRxiv · 10.1101/2022.07.13.499900

Interactive analysis of single-cell data using flexible workflows with SCTK2.0

Wang, Y.·Sarfraz, I.·Hong, R.·Koga, Y.·Akavoor, V.·Cao, X.·Alabdullatif, S.·Pervaiz, N.·Zaib, S. A.·Wang, Z.·Jansen, F.·Yajima, M.·Johnson, W. E.·Campbell, J. D.
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Abstract

Analysis of single-cell RNA-seq (scRNA-seq) data can reveal novel insights into heterogeneity of complex biological systems. Many tools and workflows have been developed to perform different types of analysis. However, these tools are spread across different packages or programming environments, rely on different underlying data structures, and can only be utilized by people with knowledge of programming languages. In the Single Cell Toolkit 2.0 (SCTK2.0), we have integrated a variety of popular tools and workflows to perform various aspects of scRNA-seq analysis. All tools and workflows can be run in the R console or using an intuitive graphical user interface built with R/Shiny. HTML reports generated with Rmarkdown can be used to document and recapitulate individual steps or entire analysis workflows. We show that the toolkit offers more features when compared with existing tools and allows for a seamless analysis of scRNA-seq data for non-computational users. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/499900v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@2a3964org.highwire.dtl.DTLVardef@1debe9org.highwire.dtl.DTLVardef@6b3a2aorg.highwire.dtl.DTLVardef@1b7bf84_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIntuitive graphical user interface for interactive analysis of scRNA-seq data C_LIO_LIAllows non-computational users to analyze scRNA-seq data with end-to-end workflows C_LIO_LIProvides interoperability between tools across different programming environments C_LIO_LIProduces HTML reports for reproducibility and easy sharing of results C_LI

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Wang, Y., Sarfraz, I., Hong, R., Koga, Y., Akavoor, V., Cao, X., Alabdullatif, S., Pervaiz, N., Zaib, S. A., Wang, Z., Jansen, F., Yajima, M., Johnson, W. E., Campbell, J. D.. 2022-07-14. Interactive analysis of single-cell data using flexible workflows with SCTK2.0. https://doi.org/10.1101/2022.07.13.499900

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