| | 1 | == Panacea xQTL review Wed 9 nov 2011 == |
| | 2 | * Data curation and annotation of the Panacea Database (joint effort) |
| | 3 | * Host project analyses: |
| | 4 | * Phase 1: Just add the R scripts as files for basic provenance |
| | 5 | * Phase 2: Being able to rerun important scripts such as sample mislabeling and QTL x Env |
| | 6 | * Phase 3: Make it easy to add and run any R script that was used |
| | 7 | * Data matrix: |
| | 8 | * Download or visualize with CytoScape |
| | 9 | * Need new view with more organization/hierarchy: group by experiment or annotation |
| | 10 | * Need to couple this hierarchy with the ability to quickly run scripts for visualization or statistics on a piece of the data |
| | 11 | * Need 'supersearch' which produces reports on concepts (ie. everything related to a marker or individual) |
| | 12 | * This should include a special 'QTL finder' tool to quickly create reports on findings using a matrix and/or traits as inputs |
| | 13 | * Focus on pathways: |
| | 14 | * Want to query pathway information for an organism from 1..N sources (GO, WormBase, KEGG.. ?) |
| | 15 | * Want to couple existing gene annotations to these pathways, semi-automatically (?) |
| | 16 | * Want to use this information to run analysis/visualizations on these batches of genes |
| | 17 | * Want to create pathway plots (biology!) with the gathered information (e.g. QTL profiles) |
| | 18 | * Want to create CytoScape graphs of e.g. correlation of the genes |
| | 19 | |
| | 20 | |
| | 21 | == EURATRANS xQTL review Wed 9 nov 2011 == |
| | 22 | * Integrate with genome browser (gBrowse, formats WGL and GFF) |
| | 23 | * Need to save any filter as a URL |
| | 24 | * Need to clarify how a tool like gBrowse can specify a 'range' in filter URL syntax and link it |
| | 25 | * Also need the 'range' to work on matrices with locus data (e.g. markers) via URL |
| | 26 | * Need to add scripts as visualizers of data: e.g. let them appear in a list of possible plot types in matrix |
| | 27 | * Search box bugs: no '_name' searches possible |
| | 28 | * Use real column names instead of labels eventually, this is still very confusing |
| | 29 | * Need for advanced matrix views: |
| | 30 | * On similar rows & columns, create 'subheaders' with multivalue display |
| | 31 | * Alternatively, matrix merge operation to concatenate them |
| | 32 | * Want to have a report on a value that appears in multiple matrices |
| | 33 | * And/or reports with plots for e.g. a marker or probe with all related information from all sources |
| | 34 | |
