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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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Add new general brain gene sets? #2

Open hagenaue opened 9 months ago

hagenaue commented 9 months ago

Space to brainstorm gene sets to add to our GMT

hagenaue commented 9 months ago

From the Enrichr website: https://maayanlab.cloud/Enrichr/#libraries

Allen_Brain_Atlas_10x_scRNA_2021 - Would just need date genes and orthologs dealt with. Allen_Brain_Atlas_down - Would also need to have fold change columns removed Allen_Brain_Atlas_up - Would also need to have fold change columns removed

hagenaue commented 9 months ago

From the Enrichr website: https://maayanlab.cloud/Enrichr/#libraries ... But would need curating for brain relevance:

GTEx_Tissue_Expression_Down MGI_Mammalian_Phenotype_Level_4_2021 - there are several of these files with different dates and I can't tell if they are independent or build upon one another, would need to be filtered down to the 117 relevant CNS phenotypes Descartes_Cell_Types_and_Tissue_2021 - looks pretty redundant with other cell type info we already have UK_Biobank_GWAS_v1 dbGaP GWAS_Catalog_2019

hagenaue commented 9 months ago

Gemma and GeneWeaver: 1) Update (and better automate...) 2) Expand to include Gemma and GeneWeaver extracted gene sets under other functional themes?