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Author Commit Message Labels Comments Date
Flashpoint
Merged obiOMIM.py latest commit
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
P-values greater than 0.001 are now displayed with regular notation in the OWSetEnrichment.py
Flashpoint
Added a documentation entry for obiDictyMutants.py
Flashpoint
Sorting according to p-values works.
Marko Toplak
Added obiDictyMutants to the documentation index.
Marko Toplak
Merged biolab/orange-bioinformatics into default
Flashpoint
Deleted redundant files on the Orange server
Flashpoint
Deleted redundant files on the Orange server
Marko Toplak
obiGeneSetSig: SPCA with threshold selection by permutation.
Marko Toplak
obiGeneSetSig: added SPCA.
Marko Toplak
OMIM: uses server files version by default.
Marko Toplak
Register already calls update_server_list internally.
Flashpoint
Added Phenotypes to DictyMutants hierarchy
Flashpoint
First attempt at configuring Orange server update
Flashpoint
DictyMutants geneset working
Flashpoint
Merged biolab/orange-bioinformatics into default
Flashpoint
Added pickling to obiDictyMutants.py, changed the URL in obiGeneSets.py's omimGeneSets()
Flashpoint
obiDictyMutants now functional
Flashpoint
obiDictyMutants now functional
Marko Toplak
obiGeneSetSig: LLR uses combined standard deviation if a standard deviation for a class was zero (this can happen as an artifict of bootstrap sampling).
Marko Toplak
obiGeneSetSig: added another method based on likelihood ratios by Su et al (2009).
Marko Toplak
Small changes to miRNA update scripts. Added title and tags to elements that were missing it.
Marko Toplak
obiGeneSetSig: CORG were build a gene too large (fixed). SetSig has the option to check if the examples are exactly alike and discard the distance between them.
Aleš Erjavec
Fixed 'Ontology' and 'Annotations' stream parsing.
Aleš Erjavec
'Ontology.__getitem__' now raises a KeyError for an unknown term id.
Aleš Erjavec
Filter out terms from the annotations that are not present in the ontology. If the annotations are newer then the ontology they can contain terms not yet present in the ontology. This leads to an error when extracting the term's parents.
Aleš Erjavec
Removed deprecated and nonfunctioning 'drawEnrichmentGraph_tostream' function.
Aleš Erjavec
obiGO code style fixes.
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