Source

orange-bioinformatics / _bioinformatics / obiGeneSets.py

Author Commit Message Labels Comments Date
Aleš Erjavec
Reverted part of changeset 857938f13079 ('load_local' definition deletion).
Flashpoint
Fixed the exception handling in obiGeneSets.py
Flashpoint
Changed the exception value from KEGG.OrganismNotFound to obiTaxonomy.UnknownSpeciesIdentifier
Flashpoint
Added an organisms shortname() function to the obiTaxonomy.py to add short names to geneset tags
Flashpoint
Added some missing info to the obiGeneAtlas.py API
Flashpoint
Version 1 of the OWCustomSet.py widget
Flashpoint
Changed the hierarchy name of Custom gene sets in obiGeneSets.py. Moved the statistics information about genesets into an info bar.
Flashpoint
Added a genesets statistics function to obiGeneSets.py. Added additional columns in OWCustomSets.py
Flashpoint
Custom genesets now use Custom Genesets hierarchy in obiGeneSets.py. Renamed OWtest.py to OWCustomSets.py and renamed the widget from test to Custom Gene Sets. Added a preview window to quickly view geneset files before importing them.
Flashpoint
The OWtest.py prototype widget for custom gene sets now correctly imports and deletes the genesets
Flashpoint
Added functionality to obiGeneSets.py to remove locally stored gene sets. Created a prototype widget OWtest.py to store and remove own gene sets. The front-end still needs work
Flashpoint
Added Reactome Pathways genesets for humans
Flashpoint
Removed obiCytobands.py and created genesets in obiGeneSets.py. updateCytobands.py saves only genesets now
Flashpoint
Added Cytobands genesets and modified obiOMIM.py. Both need some extra work.
Flashpoint
Added Phenotypes to DictyMutants hierarchy
Flashpoint
First attempt at configuring Orange server update
Flashpoint
DictyMutants geneset working
Flashpoint
Added pickling to obiDictyMutants.py, changed the URL in obiGeneSets.py's omimGeneSets()
Flashpoint
Added obiDictyMutants.py
Marko Toplak
Fixed update scripts for MeSH, GO, HomoloGene, NCBI_geneinfo, OMIM, PPI. Moved wget to Orange.utils.
Marko Toplak
Removed the old version of obiKEGG. Renamed obiKEGG2 -> obiKEGG.
Marko Toplak
Fixes for obiGeneSets. Compatible files were generated and uploaded to SF.
Marko Toplak
Classes for storing gene set data moved to Orange.bio.geneset. obiGeneSets adapted to make new pickled classes.
Marko Toplak
Speed up of setsig (obiGeneSetSig).
mitar
Fixing some imports. Marking widgets as prototypes.
mitar
Restructuring because we will not be using namespaces.