README.md

Knowledge Base

All lab work-related knowledge we gather (not code)

Collections

• Awesome Single-cell: list of almost all single-cell tools
• Single-cell RNA-seq analysis best practices from Theis lab
• Single-Cell Tutorial from Theis lab
• Single-Cell Introduction course from Hemberg lab

Tools to use

Validated

Didn't pass validation

• CellAssign: automated annotation based on provided markers. Requires to install tensorflow on R. Didn't manage to install it on the server (@vpetukhov).
• Garnett: automated annotation based on provided markers. Tried on epilepsy data, quality was too low to use (@vpetukhov). Maybe could work on simpler datasets.

Not tested

• scfind: tool from Hemberg lab, which allow to look for markers in the published atlases. Should simplify annotation.