Will a Xena private hub work for your data? Xena is very flexible with regards to data type. You can load most types of genomic or phenotype data into UCSC Xena. That is to say, if we display it, you can load it. Browse some examples on our
https://xenabrowser.net/heatmap/?bookmark=80d9c57b471b654cc569d4ceb44e6591 About The Transcript View shows transcript-specific expression or isoform percentage for 'tumor' TCGA data and 'normal' GTEX data. It allows you to compare the distribution of these values for two groups of samples. This tool was created by Akhil Kamath as part
If you want to run a hub that is accessible to others at your institute, you will want to download the jar file, here: https://genome-cancer.ucsc.edu/download/public/get-xena/ucscxena0220.tar.gz to your server host behind the firewall. The jar file is cavm-0.22.0-standalone.
Significant difference in overall survival between TERT over and under-expressed patients in TCGA lower grade glioma cohort https://xenabrowser.net/heatmap/?bookmark=7a0381a686a2f77ebdbdc41d818e825d Stratify your samples by any data (e.g. expression, copy number, subtype, age, etc) and determine if there is a statistically significant survival difference. Start
We just published the python package, xenaPython, for accessing and pulling data from any of our Hubs. A big thank you to GiriB and souravsingh for their work on this project! Installation pip install xenaPython pip install --upgrade xenaPython Usage import xenaPython as xena Example >>>