icbi-lab / infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

https://infercnvpy.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

122 stars 27 forks source link

Adding copykat cell.line parameter? #123

Closed josephreplogle closed 4 months ago

josephreplogle commented 4 months ago

Description of feature

copykat has added a mode for cell line data that has only aneuploid or diploid cells. This mode is called by setting the parameter cell.line="yes" while the default for tissue samples is cell.line="no". Is it possible to add this parameter as an option in infercnvpy.tl.copykat? Thanks!

From copykat:

' @param cell.line if the data are from pure cell line,put "yes"; if cell line data are a mixture of tumor and normal cells, still put "no".

grst commented 4 months ago

happy to accept a PR

josephreplogle commented 4 months ago

thanks, PR in