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sanderlab / scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data
http://www.sanderlab.org/scPerturb/
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Missing data of specific dataset #5

Closed siduanmiao closed 1 month ago

siduanmiao commented 1 year ago

Hello:

Recently I use your dasaset and I have some questions.

First, I want to use the data of paper 'Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens', so I download your data of "DixitRegev2016.h5ad" from https://zenodo.org/record/7278143#.Y37ubxRByUn, but I find that you only supply the data of GSM2396860_K562_TFs__High_MOI in this .h5ad file. It's strange because in your supplymentary table of Dataset information, you said this contains the data of BMDC and K562 Tissues, but there just a subset of data from K562.

Then I check your source code of scPerturb/dataset_processing/DixitRegev2016.py, and I find you put the data of GSM2396858_K562_TFs__7_days, GSM2396859_K562_TFs__13_days and GSM2396860_K562_TFs__High_MOI into a dict adatas which is contacted to superdata, but finally you saving the adata which just anndata of GSM2396860_K562_TFs__High_MOI .

Hopefully you can tell me know where is the BMDC dataset and whether the code really have some mistakes.

tessadgreen commented 1 month ago

Resolved, updated scripts now on scPerturb and updated data will be included in the forthcoming Zenodo version 1.4