ucsc-xena-geneset v0.3.3

Xena Gene Sets

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

Further documentation

To Run

npm install

npm start

To Build

npm run build

Examples

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

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