Test recipes

[sreichl]

The goal is to have all recipes tested by someone else than me and on other/their own data.
Let's collect here, when you have successfully used (parts of) a recipe and on what kind of data (no details, bc this is public).

• RNA-seq Analysis Recipe
• ATAC-seq Analysis Recipe
• Integrative Analysis Recipe
• scRNA-seq Analysis Recipe
• scCRISPR-seq Analysis Recipe

[sreichl]

• RNA-seq Recipe (without fetch-ngs)
  • mouse structural cells across organs
  • human (un-)stimulated THP-1 cells/MDM
• pseudobulk RNA-seq Recipe (based on scRNA-seq data)
  • three public human cancer datasets (only spilterlize_integrate)
  • mouse brain cells (ISTA collabs)
  • glioblastoma project (Bonn collab)

[bednarsky]

I have used both recipes multiple times, with some previous versions, but single cell RNAseq also with most recent versions now).

[sreichl]

I have used both recipes multiple times, with some previous versions, but single cell RNAseq also with most recent versions now).

both? Do you mean the same as me? Please specify always the exact recipe (I have added a list to the top for me to tick off when sufficiently tested).

[sreichl]

@burtonjake please report your experiences/testing.

[bednarsky]

I have also used the integrative recipe without any issue!

[sreichl]

@burtonjake haven't you used the ATAC-seq Analysis Recipe in some projects?

[sreichl]

• scCRISPR-seq Analysis Recipe
  • 2 CROP-seq screens in (un)stimulated THP-1 cells

[sreichl]

• scRNA-seq Analysis Recipe (TDB)
  • TSC-CRC data