Feat gsc obj - Githubissues

cnio-bu / beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

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Feat gsc obj #38

Closed SGMartin closed 2 years ago

SGMartin commented 2 years ago

Briefly, this PR:

Separates GenerateGenesets in two functions: GenerateGenesets for GMT files and GetCollection for our pre-generated collections.
Generates Genesets objects for PSc, SSc and DDS collections so that GetCollection may consume them.
Allows users to use down genesets ending in _DN and not just _DOWN, just like in MsigDB.
Separates drugInfo in four tables: IDs, Synonyms, Targets, MoAs, according to the new specs.

What's left:

Testing
Adding SSc-related drugInfo once the manual curation is finished.
Change the docs and tutorials to reflect the changes to GenerateGenesets

Going forward...:

It might be a good idea to transform "pathways" into its own collection and refactor GetCollection accordingly.
Add dependencies collection.

mj-jimenez commented 2 years ago

Point 2. is now included in this same PR. Thanks @SGMartin!