search

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

stable release #121

Open wangjiawen2013 opened 6 months ago

wangjiawen2013 commented 6 months ago

Description of feature

Hi, Thanks for such a great python package ! I want to try using infercnvpy to analyze my single cell data. I notice that there is a warning message on infercnv github:

** WARNING:

This package is still experimental. The results have not been validated, except in that they look similar, but not identical, to the results of InferCNV. **

Is it stable now and could we use infercnvpy in our work now ?

grst commented 6 months ago

Well, it has been around for a while now and is fairly widely used, so if its results were complete garbage somebody would hopefully have noted by now.

It is still the case that there's no publication, and we did not benchmark it against a gold-standard, or against other methods. There's also no plan from our side to pursue this currently.

stela2502 commented 1 month ago

Just a simple follow up question - why? Why do you not plan to at least compare the results to the R implementation? That should be straight forward - or? If you do not at least do that - how are you developing this tool? You statement " and is fairly widely used" - would you mind backing that up?

Thank you!

grst commented 1 month ago

The usual... this was a side project during my PhD -- I changed jobs since and don't have the time to further pursue this project, except for fixing critical bugs or merging pull requests.

If you want to compare it to the R version and document the results, I'm happy to accept a PR to the documentation.

You statement " and is fairly widely used" - would you mind backing that up?

The project has 119 stars on GitHub and 38k downloads on PyPI. Of course both are imperfect metrics.