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README.md

XenaGoWidget

React widget for analyzing expression of tissue samples within a pathway or set of genes.

Build Status

Further documentation

To Run

npm install

npm start

To Build

npm run build

Examples

Demo: http://xenademo.berkeleybop.io/xena/

Bladder example BRCA example Meso example

TODO

  • add a view in Xena to new Tab #1
  • put gene selection below pathway selection (and then only show the tissue view for genes) #2
  • side-by-side comparison of different analysis #4
    • provide statistics for comparisons

Data TODO

  • add cell-lines
  • add expression data
  • integration with Viper functional analysis
  • add outlier pathways

Possible TODO

  • allow multiple selection of genes / pathways with statistics (gene enrichment)
    • provide combined statistics matches
    • (allow visible selection of fields)
    • put a control / display canvas on top of another one?
  • allow selection of multiple cohorts (displayed vertically)
  • allow selection of different criteria for scoring
  • add different (drill-down) filters for scores, etc.
  • allow different ways to shade, including z-score, only percentage, etc. etc.
  • allow creation of custom pathways sets by selecting available genes (with lookup)
  • allow hiding pathways
  • show camplot
  • show annotations for hovered / selected (are these the functional annotations?)
  • integrate as new Xena page

Important biological questions

  • what genes are involved / dominant in these pathways for 'X' affects
  • what is the combined affect of these genes on various pathways for this set of selected genes
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