https://hivelab.biochemistry.gwu.edu/wiki/index.php?action=history&feed=atom&title=TCGA_Additional_Information 2026-05-26T17:18:01Z Revision history for this page on the wiki MediaWiki 1.42.1 https://hivelab.biochemistry.gwu.edu/wiki/index.php?title=TCGA_Additional_Information&diff=26&oldid=prev 2024-09-30T23:38:48Z

<p>Initial edit</p> <p><b>New page</b></p><div>Go to [https://mybinder.org/ MyBinder].<br /> <br /> For ‘Github repository name or URL’, enter https://github.com/isb-cgc/ISB-CGC-Demos, then click ‘Launch’.<br /> <br /> The methods in this tutorial were used to generate the R scripts used to download the data.<br /> <br /> [https://github.com/GW-HIVE/biomuta-old/blob/master/pipeline/download_step1/tcga/get_field_names.R get_field_names.R]<br /> <br /> Download a list of all field names for the mutation data, many fields are excluded in the mutation downloader script.<br /> <br /> [https://github.com/GW-HIVE/biomuta-old/blob/master/pipeline/download_step1/tcga/TCGA_clinical_info_download.R TCGA_clinical_info_download.R]<br /> <br /> Download clinical information for all patients included in the mutation file download.<br /> <br /> The downloaded file will contain both sample ID and patient ID, that can be mapped together in the final mutation file to calculate patient frequency for mutations from TCGA.<br /> <br /> [https://github.com/GW-HIVE/biomuta-old/blob/master/pipeline/download_step1/tcga/get_field_names_clinical_info.R get_field_names_clinical_info.R]<br /> <br /> Download a list of all field names for the corresponding clinical data, many fields are excluded in the clinical information downloader script.</div>

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