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### From Robel
Hi Jie,
The file name (before the first ".") is the patient identifier -- you just need to download another file that matches that patient id to sample_id and then to cancer type. I…
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https://genie-public-beta.cbioportal.org/study/summary?id=brca_akt1_genie_2019%2Claml_tcga_pan_can_atlas_2018%2Cacc_tcga_pan_can_atlas_2018%2Cblca_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018…
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## **Objective**: To replicate the BioMuta pipeline to generate a dataset as close as possible to the current BioMuta dataset.
**Presentation Shared with meeting notes**: https://docs.google.com/pr…
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Based on the tutorial "Tutorial-Processing WSIs for MIL" and its recommended parameters, I followed the workflow to extract patches and generate a MIL dataset using CLAM. Then, I used CTransPath to ex…
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## TCGA heatmap has a couple issues that need to be addressed:
- [ ] Make sure we are using the right TCGA MAF file (i.e: not CRCh37)
- [ ] Filtering out mutations that do not impact MANE transcript…
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# primary tasks
- [x] download TCGA MAF files
- [x] Map TCGA rows to proteins from our datasets
- DONT INCLUDE KIBA UNTIL WE GET ALL AFLOW CONFS (to ensure consistent test sets and so we don't …
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Error occurred:
Prov-gigapath main \ finetune \ training -->evaluate function
```
def evaluate(loader, model, fp16_scaler, loss_fn, epoch, args):
model.eval()
# set the evaluation re…
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Hi @clemsgrs , I encountered errors while extracting patches with hs2p on TCGA NSCLC dataset, making it impossible to tile some slides. The errors are detailed in the attached `process_list.csv`. Coul…
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> auc_dis_all(all.auc.1y,
+ dataset = names(list_train_vali_Data),
+ validate_set=names(list_train_vali_Data)[-1],
+ order= names(list_train_vali_Data),
+ …
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I have a question on downloading TCGA data. I used the gdc command line tool to download the WSIs for BRCA. However, a significant number of svs files did not download correctly, resulting in a lot of…