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ucscXena / ucsc-xena-client

Functional genomics browser
Apache License 2.0
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xena gene page #135

Open jingchunzhu opened 7 years ago

NikolayOG commented 7 years ago

I would like to work on this issue. Can you give me more information?

jingchunzhu commented 7 years ago

@NikolayOG suggestion: first know how to use the xena browser app, pull up "TCGA Pan-Cancer (PANCAN)" cohort, add three columns: gene expression, somatic mutation and phenotype/primary disease columns.

The goal is that an url https://xenabrowser.net/heatmap/?gene=TP53 will automatically give this view below: image

We will hard-code the cohort, default gene expression, and default somatic mutation dataset, and default phenotype data parameters.

NikolayOG commented 7 years ago

I am sorry about the long delay it was due to personal matter. The way I see the project : "Explore new method of visualization pathway perturbation" is that I have to analyze and compare DNA data from healthy people and people with caner. See which part of the DNA is possible causation for cancer taking into account the noise in the data. Then see for which protein is that DNA part responsible for. Then see in which pathway is this protein and visualize that.

2017-03-05 23:54 GMT+00:00 jingchunzhu notifications@github.com:

suggestion: first know how to use the xena browser app, pull up "TCGA Pan-Cancer (PANCAN)" cohort, add three columns: gene expression, somatic mutation and phenotype/primary disease columns.

The goal is that an url https://xenabrowser.net/heatmap/?gene=TP53 will automatically give this view below https://xenabrowser.net/heatmap/?bookmark=2a4299d9899031787098f4e789d4c319 : [image: image] https://cloud.githubusercontent.com/assets/999493/23592808/0f7dbefa-01bb-11e7-8640-6ecc65587a35.png

We will hard-code the cohort, default gene expression, and default somatic mutation dataset, and default phenotype data parameters.

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