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hagenaue / Brain_GMT

Code and documentation for the brain-related gene set (Brain.GMT) curation project
MIT License
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Fix bugs in GMTs (v1, v2) #1

Closed hagenaue closed 6 months ago

hagenaue commented 12 months ago

The bugs are in the mouse and human versions ... first I need to find them.

hagenaue commented 12 months ago

Mouse: "Zeisel_CA1PyramidalIndex_FixedDateGenes.csv" - this seems to just be made into the correct formatting for mice (it was derived from mice, but the gene symbols are in all caps...)

Relevant code document: 08_DeterminingOrthologs_CustomGeneSets.R 17_CombiningGMTs.R

hagenaue commented 12 months ago

Mouse: "CombinedHCspecific_Mouse.gmt.txt" - this seems to just need to be made into the correct formatting for mice (it was derived from mice, but the gene symbols are in all caps...)

Relevant code document: 09_DeterminingOrthologs_ImportedGMTs.R 17_CombiningGMTs.R

hagenaue commented 12 months ago

Human and Mouse: The Gemma Rat GMT needs human ortholog and mouse ortholog versions (I'm not sure why - the Gemma Mouse and Human GMTs were converted to orthologs, but not the rat)

hagenaue commented 12 months ago

Human and Mouse: The GeneWeaver Rat GMT needs human ortholog and mouse ortholog versions (I'm not sure why - the GeneWeaver Mouse and Human GMTs were converted to orthologs, but not the rat)

hagenaue commented 12 months ago

Mouse: Combine all of the individual .GMTs into a single MouseBrain.GMT Human: Combine all of the individual .GMTs into a single HumanBrain.GMT

hagenaue commented 6 months ago

All resolved