Interactive single cell RNA-Seq analysis with Single Cell Toolkit (SCTK)
Files
Poster .pdf file
Date
2019-05
DOI
Authors
Johnson, W. Evan
Jenkins, David
Khan, Mohammed Muzamil
Faits, Tyler
Zhang, Yuqing
McFarlane, Ada
Zhao, Yue
Campbell, Joshua David
Yajima, Masanao
Version
OA Version
Citation
Abstract
I will present the Single Cell Toolkit (SCTK), an R package and interactive single cell RNA-sequencing (scRNA-Seq) analysis package that provides the first complete workflow for scRNA-Seq data analysis and visualization using a set of R functions and an interactive web interface. Users can perform analysis with modules for filtering raw results, clustering, batch correction, differential expression, pathway enrichment, and scRNA-Seq study design. The toolkit supports command line or pipeline data processing, and results can be loaded into the GUI for additional exploration and downstream analysis. We demonstrate the effectiveness of the SCTK on multiple scRNA-seq examples, including data from mucosal-associated invariant T cells, induced pluripotent stem cells, and breast cancer tumor cells. While other scRNA-Seq analysis tools exist, the SCTK is the first fully interactive analysis toolkit for scRNA-Seq data available within the R language.
Description
License
Attribution 3.0 United States