Creating a databse of bone biomarkers for mouse by combining multiple sources.
Download mouse cell markers, save as csv to
/CellMarker2_0/Cell_marker_Mouse.csv
Download single-cell markers, save as csv to
/CellMarker2_0/Cell_marker_Seq.csv
Download M8: cell type signature set and save it as
/MSigDB/m8.all.v2023.1.Mm.symbols.gmt
Download PanglaoDB for all cell types unzip, and save it as
/PanglaoDB/PanglaoDB_markers_27_Mar_2020.tsv
Download mouse Knowledge channel and save as
/TISSUES/mouse_tissue_knowledge_full.tsvDownload mouse Experiment channel and save as/TISSUES/mouse_tissue_experiments_full
Using /R_scripts/process_databases.R script extract bone-relevant features from all downloaded datasets and create bone-relavant marker database (or just get the processed TSV file here).
R script /R_scripts/make_database_as_lists.R takes the full database and reshapes it into lists (used in enrichment analysis of ranked lists by for example fgsea). The final lists are following:
- list with markers for individual cell types: /BONE_DATABASE_lists/bone_cellType.Rdata
- list with markers for individual cell types separated by source database: /BONE_DATABASE_lists/bone_cellType_and_sourceDB.Rdata
- list with markers for individual tissues: /BONE_DATABASE_lists/bone_tissue.Rdata
- list with markers for individual tissues separated by source database: /BONE_DATABASE_lists/bone_tissue_and_sourceDB.Rdata