scverse / pertpy

Perturbation Analysis in the scverse ecosystem.

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

MIT License

132 stars 20 forks source link

Datasets #18

Closed M0hammadL closed 1 year ago

M0hammadL commented 3 years ago

We have multiple datasets that we need to prepare:

multimodal single-cell CRISPR screens:

[ ] https://nature.com/articles/s41588-021-00779-1
[ ] https://www.nature.com/articles/s41588-021-00778-2 (mixscape)
[ ] Christians Bocks dataset (we already have it)
[ ] Hanifta large scale cite-se datasets with covid 19 (Chris has the data, large-scale CITE-seq, maybe goo to show scale)

Uni Modal KO datasets #17

[ ] Norman et al. https://science.sciencemag.org/content/365/6455/786.abstract (we have)

Normal scRNA-seq:

continues covariates to test auger ( https://science.sciencemag.org/content/367/6473/45, we have the data)
cross-species dataset with continuous-time but only perturbation (https://www.nature.com/articles/s41586-018-0657-2, we have the data)

RNA velocity perturbation analysis

[x] dataset which was analyzed augor protocol paper

ilibarra commented 3 years ago

[x] Prepare the mixscape toy dataset and upload it into a function to the pertpy.datasets equivalent. (me)

M0hammadL commented 2 years ago

the datasets could be downloaded from here : |https://github.com/facebookresearch/CPA

https://dl.fbaipublicfiles.com/dlp/cpa_binaries.tar

ilibarra commented 2 years ago

note: The cpa_binaries.tar file is ~15GB, so probably call from curl or wget to the destination folder, instead of direct download.

Zethson commented 1 year ago

Tracked in some GDoc