search

theislab / scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.
MIT License
66 stars 27 forks source link

data sets available? #11

Closed zia1138 closed 2 years ago

zia1138 commented 3 years ago

Great job on the scib pipeline. I imagine it was a big headache getting all of these methods to work. I was wondering if the benchmark data set h5ad files were available for download? They seem to be hard coded in config/reproduce_paper.yaml Thanks!

LuckyMD commented 3 years ago

Hi @zia1138,

The data are all on the figshare here: https://figshare.com/articles/dataset/Benchmarking_atlas-level_data_integration_in_single-cell_genomics_-_integration_task_datasets_Immune_and_pancreas_/12420968

This is in the revised manuscript... that should be out soon I hope :). We should probably also add this to the README... @mumichae could you add the link?

Ooh... I think mouse brain is not on there yet, because I haven't left my laptop on overnight to upload this yet :/. If you need it urgently I can upload soon. If not, I'll keep it in the middle of my todo list.

And yes... not always easy to get running, but a lot of that was also our fault with R and python methods in the same framework. If you just want to run the methods ad-hoc, it is easier i think ;).

zia1138 commented 3 years ago

No hurry on my end. Thank you again for the great work. It's nice to see a careful evaluation of all of these approaches.

LuckyMD commented 3 years ago

Thanks :).

Noelandinho237 commented 3 years ago

Where is it

LuckyMD commented 3 years ago

Mouse brain is still not uploaded. The others are at the link above.