I have a raw un-normalized data array which is oriented genes (column) by cell (row). Does scanpy read the file in this way when loading the data or do I need to transpose to cell (columns) by gene (rows)?
Hi!
AnnData reads features/genes in columns and cells in rows, so you do not need to transpose.
Best, Jesko
1 Like
This just as a random example of Scanpy mentioning this layout in one of their functions: scanpy/_simple.py at d9526825b02ab0a53ac6702474c14b23e0fa2604 · scverse/scanpy · GitHub