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README.md
# Single Cell TK <!-- badges: start --> [![R-CMD-check](https://github.com/compbiomed/singleCellTK/workflows/R-CMD-check/badge.svg)](https://github.com/compbiomed/singleCellTK/actions) [![codecov](https://codecov.io/gh/compbiomed/singleCellTK/branch/master/graph/badge.svg)](https://codecov.io/gh/compbiomed/singleCellTK) <!-- badges: end --> The Single Cell ToolKit (SCTK) is an analysis platform that provides an **R interface to several popular scRNA-seq preprocessing, quality control, and visualization tools**. SCTK imports raw or filtered counts from various single cell sequencing technologies and upstream tools such as 10x CellRanger, BUStools, Optimus, STARSolo, and more. By integrating several publicly available tools written in R as well as Python, SCTK performs extensive quality control measures including doublet detection and batch effect correction. Additionally, SCTK summarizes results and related visualizations in a comprehensive R markdown and/or HTML report. SCTK provides a standardized single cell analysis workflow by representing the counts data and the results using the [SingleCellExperiment](https://www.bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) R object. Furthermore, SCTK enables seamless downstream analysis by exporting data and results in flat .txt and Python Anndata formats. A comprehensive list of available functions is listed in the Reference section. (add link here) ## Installation Detailed intstructions on how to install singleCellTK are available in the link below: (add link here) ## Features ## Report Issues (add link here to issues)