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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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> 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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![微信图片_20240717144313](https://github.com/user-attachments/assets/1ccdd956-6b4f-4ec9-9095-292bc43fa549)
There seems to be a problem when it comes to gbm methods.It's not like a mistake because th…
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Hello, thank you for the wonderful tool. First time posting, so please let me know if this issue has been solved elsewhere (I couldn't find) or if more information would be helpful. I have been using …
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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…
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Dear Greg - thanks for your continued work on this and for this follow up paper with updated pipeline. I'm the lead author of [Hermida et al. Nat Commun 2022](https://www.nature.com/articles/s41467-02…
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Could you please provide the `TCGA_RCC` and `TCGA_Lung` datasets through an alternative method, such as Google Drive? I have encountered difficulties downloading them from the provided [link](https://…
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Hi,
I've practiced the model training following the tutorial you provided.
The gdcCancer.bb file was downloaded from the link in the tutorial, and later was converted to bed file using bigBedToB…
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- [ ] #120
- [x] test set level table
- [x] gene level cancer type heatmap
- [x] patient specific bar graph stratified by cancer type
![image](https://github.com/jyaacoub/MutDTA/assets/50300488/…