Add copykat to tutorial
grst opened this issue · comments
Show that tl.copykat can work as drop-in replacement for tl.infercnv
could add parameter -norm.cell.names?
would it be possible to add the cnv_result$prediction to the adata.obs['copyKat']?
In principle, yes.
I currently don't have time to look into it, but feel free to submit a PR with your suggestions.
On top of that, we were experiencing a few issues with copykat, in particular copykat applies its own cell filtering strategy, s.t. the output matrix does not necessarily fit into the original adata object.
Additionally we started investigating SCEVAN which according to their preprint has superior performance over copykat.
good to know, i submitted a PR but seems to fail on generating the docs.
Superseded by #28