# Single Cell TK
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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)
More information about the toolkit can be found at the toolkit [homepage](https://camplab.net/sctk/).
## Installation
Detailed intstructions on how to install singleCellTK are available at the link below:
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## Features
The toolkit offers mulitple ways to analyze your single cell data both through the R console, commandline (QC) and graphical user interface with the ability to use a large number of algorithms from both R & Python integrated within the toolkit.
#### Console Analysis
Traditional analysis of single-cell RNA-seq data can be performed in the R console using wrapper functions for a multitude of tools and algorithms.
#### Interactive Analysis
The shiny app allows users without programming experience to easily analyze their single cell RNA-seq data with a graphical user interface.
#### Reports
Comprehensive html reports developed with rmarkdown allows users to document, explore, and share their analyses.
#### Interoperability
Tools from both R and Python can be seamlessly integrated within the same analysis workflow.
More information about the toolkit can be found at the toolkit [homepage](https://camplab.net/sctk/).
## Report Issues
If you face any difficulty in installing or using the toolkit or have identified a bug in the toolkit, please feel free to open up a [GitHub issue](https://github.com/compbiomed/singleCellTK/issues).