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Hey guys, congratulations for your paper. I would like to rerun your analysis with a different pathway database. Could you please point me to the scripts to rerun the analysis?
Thank you in advance,
…
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Example command:
```
(base) $ ./jsonschemagraph/jsonschemagraph gen-graph iceberg/schemas/graph/Patient.yaml TCGA-ESCA/META/Patient.ndjson
graph Patient
Loaded [Patient]
Writing: graph/Patient…
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Hi,
Not an issue, but a question regarding TCGA batch-corrected expression data. Where i can download the most recent batch corrected pancancer TCGA RNA-seq expression data? Not individual cancers,…
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Hi all,
I'm trying to extract the TDA signatures that you generated for the TCGA PanCancer BRCA cohort. It seems like the `tcga_recurrence_pam50_vs_tdasignatures.csv` file should contain this infor…
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Hi! Thanks for your great work!
May I ask you a question?
Is the classification task for dataset TCGA-NSCLC still a binary classification task (the same as binary classification task for dataset CAM…
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I think that the control is the best. How to generate the gtex_ctrl_db and tcga_matched_control_junction_count.h5ad, Maybe a number of *.fasq in tcga and GTEx analysed by SNAF first?
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Thank you for your wonderful work!
I encountered an issue while running mmp_visualization.ipynb. Although I successfully ran MMP and obtained the results, the notebook requires reading an h5_feats_…
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Hey,
where can I download the data to redo the predictions? E.g.:
data/TCGA_GDSC/gdsc_exprs.csv
data/gdsc1_sensitivity_update.csv
data/path_embed_processed.csv
Thanks
Pascal
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see e.g. https://www.cbioportal.org/patient/pathologyReport?studyId=ucec_tcga_pub&caseId=TCGA-BK-A0CC
inodb updated
5 months ago
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Dear authors, I am now reading your paper "Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response", it is an amazing and impressive work and…