Index

A

alt_id (goscripts.obo_tools.goTerm attribute)

annotateOutput() (in module goscripts.enrichment_stats) assign_depth() (in module goscripts.obo_tools)

B

buildGOtree() (in module goscripts.obo_tools)

C

children (goscripts.obo_tools.goTerm attribute) cleanGafTerms() (in module goscripts.gaf_parser)

completeChildHierarchy() (in module goscripts.obo_tools) countGOassociations() (in module goscripts.enrichment_stats) createSubsetGafDict() (in module goscripts.gaf_parser)

D

depth (goscripts.obo_tools.goTerm attribute)

E

enrichmentAnalysis() (in module goscripts.enrichment_stats)

enrichmentOneSided() (in module goscripts.enrichment_stats)

F

filterOnNamespace() (in module goscripts.obo_tools)

G

goCount (goscripts.obo_tools.goTerm attribute) goscripts (module) goscripts.enrichment_stats (module)

goscripts.gaf_parser (module) goscripts.genelist_importer (module) goscripts.obo_tools (module) goTerm (class in goscripts.obo_tools)

I

id (goscripts.obo_tools.goTerm attribute) importGAF() (in module goscripts.gaf_parser)

importGeneList() (in module goscripts.genelist_importer) importOBO() (in module goscripts.obo_tools) isValidSubset() (in module goscripts.genelist_importer)

M

multipleTestingCorrection() (in module goscripts.enrichment_stats)

N

name (goscripts.obo_tools.goTerm attribute)

namespace (goscripts.obo_tools.goTerm attribute)

P

parents (goscripts.obo_tools.goTerm attribute)

propagateParents() (in module goscripts.obo_tools)

R

recursive_children (goscripts.obo_tools.goTerm attribute) recursive_parents (goscripts.obo_tools.goTerm attribute)

recursiveTester() (in module goscripts.enrichment_stats) reportMissingGenes() (in module goscripts.genelist_importer)

S

set_namespace_root() (in module goscripts.obo_tools)