cancer-data

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exploring the data

3

An issue has been raised in the meeting today regarding visualizations of the clinical data. Other data viz are also considered. However, more immediately, we need viz schemes of the...

ypar

Gene names converted to dates in Xena's PANCAN_mutation dataset

5

I've noticed that some gene names have been converted to dates in `PANCAN_mutation` ([version info](https://github.com/dhimmel/cancer-data/blob/ffe66ab26000379adcd7138b8ff39920d4692ef1/download/PANCAN_mutation.json), [Xena Browser](https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.PANCAN.sampleMap/PANCAN_mutation&host=https://tcga.xenahubs.net)). Here are some of the effected rows: | sample | chr | start...

dhimmel

Which types of mutation effects should be ignored?

5

The `PANCAN_mutation` dataset ([online doc](https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.PANCAN.sampleMap/PANCAN_mutation&host=https://tcga.xenahubs.net)) contains several types of mutations under the `effect` column. My processing of the dataset ([notebook](https://github.com/dhimmel/cancer-data/blob/8c7a8023d3be838c77e1dfa8139ec5c345039fa0/2.TCGA-process.ipynb)) yielded the following mutation effect and frequencies (as counts and...

dhimmel