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What are the chances the TCGA data used in the README or the code used to collect it from TCGAbiolinks could be made available?
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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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Hi,
Congrats on your accepted work! I'd have some questions to understand the model architecture and performance better.
- What patch encoder did you use in the CLAM baseline? Is it based on Re…
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http://localhost:8082/study/summary?id=crc_public_genie_bpc%2Cacc_tcga_pan_can_atlas_2018
Filter on cancer study and you'll get a sample list filter.
(make sure this doesn't happen in legacy a…
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Hi,
Thanks for a very comprehensive resource! I have compiled [a list](https://www.dropbox.com/s/b6ny549bs8mb6f9/tcga_clinical_tissue_diagnosis.v18_20190708.tsv?dl=0) of unique diagnoses assigned to …
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The plan for updating the BioMuta pipeline was to be given to EBI for them to generate the datasets. We are still in talks with them but the most important issue is the disease and clinical patient da…
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lgggbm_tcga_pub ('Merged Cohort of LGG and GBM (TCGA, Cell 2016)') includes data from both LGG & GBM cohorts, so should appear as redundant when any of those are selected. Currently it doesn't get fla…
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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 Sam, its me again here.
Tried running the program again with TCGA samples, but unfortunately immediately ran into this new error.
When running the preprocessing, I realise that the tag direc…