scMINER Full Documentation

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scMINER documentation website was set up using pkgdown package. It contains four sections:

• Home Page: built from README.md by pkgdown package
• Quick Tutorial: built from vignettes by pkgdown package
• Full Documentation: build and maintained independently with bookdown package
• Functions: built from man/Rd files by pkgdown package

This repository is used to maintain the Full Documentation of scMINER.

When some changes are made to scMINER R package:

• If there is nothing to modify in the Full Documentation, just re-build the documentation website by:

  1. Update the documentation if the codes of functions are modified;
  2. In main repository directory (containing index.html file) of scMINER project, run pkgdown::build_site() or Addins-Build pkgdown. This will update some files in /docs.
  3. Git commit and push to GitHub. The website page should automatically renewed.

• If the Full Documentation needs to be modified, then you will need update the book here before you re-build the documentation website:

  1. Modify the r markdown files accordingly;
  2. In main repository directory (containing index.html file) of this project, run bookdown::render_book() or Build-Build Book. This will update some files in /docs.
  3. Copy all updated files in /docs into scMINER/docs/bookdown folder. We specified bookdown/index.html as the href of Full Documentation.
  4. Re-build the documentation website as described above.