bryanhe / cloudpred Goto Github PK

Hi,

I enjoyed this paper and was hoping to play around with the simulation platform. I think the scripts/run_all.sh script is currently missing, so I tried to first run scripts/synthetic.py. That script seems to rely on npz fils in a data folder not included in the repo, with the real scRNA-seq from the 10 different cell types. Is this data publicly available?

Thanks,
Nalini

Hello,

I would use your software but the input format is a bit confusing. From the simulated data I could guess the following format:
Xall=[[count_matrix_class1,y_label,None],[count_matrix_class2,y_label,None]], but it is not clear None should refer to what since --figroot doesn't work with None value. I would be grateful if you provide more details on this issue.

Thank you,

Amina

Hi,

I'm interested in testing your algorithm with my own data. Could you please provide a description of the required input format for the data and metadata? It would also be very helpful to have some documentation on the required (and optional) input parameters.

Thanks,
Sarah

Hello! In https://github.com/bryanhe/CloudPred/blob/master/cloudpred/main.py#L168 , and in several following strings model variable is used for drawing plots, instead of best_model which is used for printing scores. I wonder, if this is intentional, or just a typo