Combination Datasets - Githubissues

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

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Combination Datasets #5

Closed MxMstrmn closed 2 years ago

MxMstrmn commented 3 years ago

Get the combination dataset from Alex for checking drug interaction (synergetic, etc.) and curate the data

M0hammadL commented 3 years ago

datasert 1, ALMANAC:

Here is the raw data : https://wiki.nci.nih.gov/display/NCIDTPdata/NCI-ALMANAC

and here is the paper : https://cancerres.aacrjournals.org/content/77/13/3564

the data is here: /storage/groups/cbm01/datasets/alexander.ohnmacht/synresp/data/ALMANAC

we have to make an h5ad file from it:

take the log of CONC for training (log o concentration)
the outcome is PERCENTGROWTH we have to predict drug a with dose x and drug b with a dose y would change PERCENTGROWTH.
we have to add a column that checks how many of cell-lines and drugs overlap with Lincs