search

bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
GNU General Public License v3.0
79 stars 15 forks source link

Output does not match #27

Open clee700 opened 1 year ago

clee700 commented 1 year ago

Hello! I had a question about the output. My output has only 'Cell Type', 'Z-score', and 'Cluster'. How do I get 'Type' and 'Times' (which are listed as part of the output on the tutorial page)? Second question, the output has several cell types for each cluster. Is it appropriate to pick the cell type with the highest Z score?

Code: python3 SCSA.py -d whole.db -s seurat -i SCSA_Markers_df.csv -k All -E -g Mouse -p 0.01 -f 1 -m txt -o SCSA_out

bioinfo-ibms-pumc commented 1 year ago

Hello, the first question, if you can get the only one cell type properly, then you can choose it directly. 'Times' was used to compare some unsure cell types. Second question, sometimes the highest Z score is good, but when the score of other cell type is near the first, you should consider with your experience.