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Welcome to the singleCellTK developers wiki! singleCellTK is a framework for incorporating different tools under unified workflows which can be run using the R console, a Shiny GUI, or within Rmarkdown reports. singleCellTK is a Bioconductor package and so all code should conform to Bioconductor standards. Please read over the Bioconductor coding style and general package guidelines before starting to write your code. The pages listed below describe requirements and suggestions specific to the singleCellTK package.

Coding environment and lifecycle

• Developer Environment Setup
• Recommended procedures for adding and checking new code (Under construction)
• Creating new releases (Only useful for singleCellTK repo managers)
• Code best practices

Adding new tools

• Writing code to incorporate new tools
• Function documentation and parameter naming standards
• Calling Python with reticulate
• Using tags with data items

Setting up a Shiny server

• Installing the SCTK Shiny app on a server
• Best practices for the Shiny GUI