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* I am currently developing a plugin that enables the user to extract pathway information directly from the Reactome MySQL database. At this moment it allows people to select the pathway of interst and do 2 types of colouring: 1) Occurence colouring, gives the node a colour according to how many times an orthologous reaction exist in other species. (white =0, redness is amount) 2) Expression colouring, gives the node a colour according to gene expression levels. (At this moment negative foldchanges are red, positive foldchanges are green) I am currently working on supporting selective colouring by usage of statistical values such as the p-value. (e.g. Only colour when p-value < 0.05) the input is file format is the same as GenMAPP uses. |
* I (Willem Ligtenberg, Eindhoven University of Technology) am currently developing a plugin that enables the user to extract pathway information directly from the Reactome MySQL database. At this moment it allows people to select the pathway of interst and do 2 types of colouring: 1) Occurence colouring, gives the node a colour according to how many times an orthologous reaction exist in other species. (white =0, redness is amount) 2) Expression colouring, gives the node a colour according to gene expression levels. (At this moment negative foldchanges are red, positive foldchanges are green) I am currently working on supporting selective colouring by usage of statistical values such as the p-value. (e.g. Only colour when p-value < 0.05) The input is file format is the same as GenMAPP uses. |
Feel free to add your plugins in development to this list.
- The MSKCC group is developing a plugin that will allow users to view expression data on BioPAX pathways from Reactome and other databases in a more user friendly way than is currently available in Cytoscape. The goal is to allow this in 2 or 3 mouse clicks with no other actions e.g. no file editing.
- I (Willem Ligtenberg, Eindhoven University of Technology) am currently developing a plugin that enables the user to extract pathway information directly from the Reactome MySQL database. At this moment it allows people to select the pathway of interst and do 2 types of colouring:
- 1) Occurence colouring, gives the node a colour according to how many times an orthologous reaction exist in other species. (white =0, redness is amount) 2) Expression colouring, gives the node a colour according to gene expression levels. (At this moment negative foldchanges are red, positive foldchanges are green)
I am currently working on supporting selective colouring by usage of statistical values such as the p-value. (e.g. Only colour when p-value < 0.05) The input is file format is the same as GenMAPP uses.
- 1) Occurence colouring, gives the node a colour according to how many times an orthologous reaction exist in other species. (white =0, redness is amount) 2) Expression colouring, gives the node a colour according to gene expression levels. (At this moment negative foldchanges are red, positive foldchanges are green)