Closed llumdi closed 1 year ago
There is a typo in the .gmt file for the neutrophils signature.
mymarkers = bc.tl.sig.read_GMT_sign(gmt_file_anno, directed=False) mymarkers['Neutrophil']
mymarkers = bc.tl.sig.read_GMT_sign(gmt_file_anno, directed=False)
mymarkers['Neutrophil']
Output: ['ELANE', 'MPO', 'PRTN3', 'CTSG', 'AZU1', 'FCGR3B CXCR2 ']
@kohleman can you fix the gmt file (besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt) so that FCGR3B and CXCR2 genes are read correctly? I though I fixed it in my last commit, but apparently not... Thanks a lot
besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt
Fixed both human and mouse
swalpe
commented
1 year ago
There is a typo in the .gmt file for the neutrophils signature.
mymarkers = bc.tl.sig.read_GMT_sign(gmt_file_anno, directed=False)mymarkers['Neutrophil']Output: ['ELANE', 'MPO', 'PRTN3', 'CTSG', 'AZU1', 'FCGR3B CXCR2 ']
@kohleman can you fix the gmt file (
besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt) so that FCGR3B and CXCR2 genes are read correctly? I though I fixed it in my last commit, but apparently not... Thanks a lot