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Dear team,
Any chance of adding TCGA annotation in the future as well ? That's very useful as well.
Regards
Najeeb
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Hi,
it is very useful package! I download fpkm gene expression data from TCGA by TCGAbiolinks package, and i try to get the immune subtypes of the LUAD samples by using this package.when i compare t…
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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/…
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Hello, I'd like to ask why, during experimentation with BCSS, it was observed that one class of predictions appears as black, although in reality the original labels were not black.
![TCGA-OL-A97C-DX…
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Hi, I am getting the following error when trying to run histoqc on .svs files.
Command:
`python -m histoqc -c v2.1 -n 3 "./input_svs_test/*.svs"`
Error:
`
2024-07-03 15:43:52,680 - INFO - --…
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fetch("https://genie-public-beta1.cbioportal.org/api/column-store/filtered-samples/fetch?", {
"headers": {
"accept": "*/*",
"accept-language": "en-US,en;q=0.9",
"cache-control": "no-cach…
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There are some vestigial endpoints for importing data from the TCGA that haven't worked since the hosting service changed. The endpoints and models associated with this should be removed.
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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 @GeorgeBatch, while running the command bash `./0-download-LUSC-and-LUAD.sh`, I encountered an issue where the WSI used for testing in DSMIL are not being downloaded. According to the documentation…