Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W A AArtGeneProductSetsAll (class in goatools.grouper.aart_geneproducts_all) AArtGeneProductSetsOne (class in goatools.grouper.aart_geneproducts_one) add_alt_goids() (in module goatools.gosubdag.go_tasks) add_children_gos() (goatools.go_search.GoSearch method) add_edges() (goatools.gosubdag.plot.go_edge.GoEdge method) add_f2str() (goatools.rpt.nts_xfrm.MgrNts method) add_to_typedef() (in module goatools.godag.typedef) add_worksheet() (goatools.wr_tbl_class.WrXlsx method) adjdir (goatools.gosubdag.go_paths.GoPaths attribute) adjust_prtfmt() (goatools.rpt.prtfmt.PrtFmt static method) all_chrints (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll attribute) all_methods (goatools.multiple_testing.Methods attribute) alpha2col (goatools.godag_plot.GODagPltVars attribute) (goatools.gosubdag.plot.go2color.Go2Color attribute) (goatools.gosubdag.plot.goea_results.GoeaResults attribute) alternatives (goatools.pvalcalc.FisherScipyStats attribute) AnnoOptions (class in goatools.anno.opts) AnnoReaderBase (class in goatools.anno.annoreader_base) AnnotationExtension (class in goatools.anno.extensions.extension) AnnotationExtensions (class in goatools.anno.extensions.extensions) argparser (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli attribute) aspect2ns (goatools.anno.init.reader_gaf.GafData attribute) B Bonferroni (class in goatools.multiple_testing) C calc_pvalue (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) calc_pvalue() (goatools.pvalcalc.FisherScipyStats method) (goatools.pvalcalc.PvalCalcBase method) calc_qval() (in module goatools.multiple_testing) chk() (goatools.anno.init.reader_gaf.GafData method) chk_associations() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.gaf_reader.GafReader method) (goatools.anno.idtogos_reader.IdToGosReader method) chk_edges() (goatools.gosubdag.go_edges.EdgesBase method) chk_edges_nodes() (goatools.gosubdag.go_edges.EdgesBase static method) chk_genes() (goatools.cli.find_enrichment.GoeaCliFnc method) chk_godag() (goatools.anno.annoreader_base.AnnoReaderBase method) chk_goids() (in module goatools.gosubdag.go_tasks) chk_kwargs() (in module goatools.gosubdag.utils) chk_qualifiers() (goatools.anno.annoreader_base.AnnoReaderBase method) chk_relationships() (in module goatools.godag.consts) chk_relationships_all() (goatools.godag.relationship_combos.RelationshipCombos method) chkaddhdr() (goatools.anno.init.reader_gaf.GafHdr method) (goatools.anno.init.reader_gpad.GpadHdr method) ClassicAlgorithm (class in goatools.goea.algorithms) (class in goatools.goea.algorithms.classic) clean_anno() (in module goatools.anno.update_association) cli() (goatools.cli.gosubdag_plot.PlotCli method) (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli method) (goatools.cli.prt_terms.PrtGOterms method) (goatools.cli.wr_sections.WrSectionsCli method) (in module goatools.cli.wr_hierarchy) CliGetGOs (class in goatools.cli.gosubdag_plot) cmpline (goatools.anno.init.reader_gaf.GafHdr attribute) (goatools.anno.init.reader_gpad.GpadHdr attribute) cmpver (goatools.anno.init.reader_gpad.InitAssc attribute) code2nt (goatools.evidence_codes.EvidenceCodes attribute) combine_nt_lists() (in module goatools.nt_utils) common_parent_go_ids() (in module goatools.semantic) CompareGOsCli (class in goatools.cli.compare_gos) convert_ints_floats() (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) count_terms() (in module goatools.ratio) CountRelatives (class in goatools.gosubdag.godag_rcnt) CountRelativesInit (class in goatools.gosubdag.godag_rcnt_init) CurNHigher (class in goatools.godag.go_tasks) D DagA (class in goatools.semsim.termwise.dag_a) DavidChartReader (class in goatools.parsers.david_chart) deepest_common_ancestor() (in module goatools.semantic) DEF_SRCH_HDRS (goatools.go_search.GoSearch attribute) default_alternative (goatools.goea.algorithms.base.GoeaAlgorithm attribute) (goatools.goea.algorithms.elim.ElimAlgorithm attribute) (goatools.goea.algorithms.ElimAlgorithm attribute) (goatools.goea.algorithms.GoeaAlgorithm attribute) default_fld2col_widths (goatools.rpt.prtfmt.PrtFmt attribute) default_fld2fmt (goatools.rpt.prtfmt.PrtFmt attribute) dflt_fmt_hdr (goatools.wr_tbl_class.WrXlsx attribute) dflt_items_p_line (goatools.gosubdag.plot.goea_results.GoeaResults attribute) dflt_outfile (goatools.cli.gosubdag_plot.PlotCli attribute) dflt_rel2scf (goatools.semsim.termwise.wang.SsWang attribute) dflt_sortby_ntgoea() (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs static method) dflt_sortby_objgoea() (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs static method) dflt_wbfmtdict (goatools.wr_tbl_class.WbFmt attribute) dflts (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot attribute) dnld_annofile() (in module goatools.associations) dnld_annotation() (in module goatools.associations) dnld_assc() (in module goatools.associations) dnld_file() (in module goatools.base) dnld_gaf() (in module goatools.base) dnld_gafs() (in module goatools.base) dnld_goa() (goatools.anno.dnld_ebi_goa.DnldGoa method) dnld_ncbi_gene_file() (in module goatools.associations) DnldGoa (class in goatools.anno.dnld_ebi_goa) do_hdr() (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) DocOptParse (class in goatools.cli.docopt_parse) download_go_basic_obo() (in module goatools.base) download_ncbi_associations() (in module goatools.base) draw_lineage() (goatools.obo_parser.GODag method) E EdgesBase (class in goatools.gosubdag.go_edges) EdgesPath (class in goatools.gosubdag.go_edges) EdgesRelatives (class in goatools.gosubdag.go_edges) ElimAlgorithm (class in goatools.goea.algorithms) (class in goatools.goea.algorithms.elim) ev2idx (goatools.evidence_codes.EvidenceCodes attribute) EvidenceCodes (class in goatools.evidence_codes) excl_flds (goatools.cli.compare_gos.CompareGOsCli attribute) exclude (goatools.gosubdag.plot.go_node.GoNode attribute) exp_elems (goatools.gosubdag.plot.go_edge.GoEdgeOpts attribute) (goatools.gosubdag.plot.go_node.GoNodeOpts attribute) exp_keys (goatools.gosubdag.gosubdag_init.InitFields attribute) (goatools.gosubdag.plot.go_edge.GoEdgeOpts attribute) (goatools.gosubdag.plot.go_node.GoNodeOpts attribute) (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot attribute) exp_kws (goatools.anno.gaf_reader.GafReader attribute) (goatools.anno.genetogo_reader.Gene2GoReader attribute) (goatools.anno.gpad_reader.GpadReader attribute) (goatools.anno.idtogos_reader.IdToGosReader attribute) exp_nss (goatools.anno.annoreader_base.AnnoReaderBase attribute) exp_numcol (goatools.anno.init.reader_gpad.InitAssc attribute) exp_qualifiers (goatools.anno.annoreader_base.AnnoReaderBase attribute) (goatools.anno.init.reader_gpad.InitAssc attribute) extract_kwargs() (in module goatools.gosubdag.utils) exts (goatools.anno.dnld_ebi_goa.DnldGoa attribute) F FDR (class in goatools.multiple_testing) fieldname (goatools.multiple_testing.Methods.NtMethodInfo attribute) fill_altgoids() (in module goatools.gosubdag.go_tasks) fill_childgoid2obj() (in module goatools.gosubdag.go_tasks) fill_main_goids() (in module goatools.gosubdag.go_tasks) fill_parentidid2obj_r0() (goatools.godag.go_tasks.CurNHigher method) fill_parentidid2obj_r1() (goatools.godag.go_tasks.CurNHigher method) fill_relationshipgo2obj() (goatools.gosubdag.go_tasks.RelationshipFill method) fill_relationshipobjs() (in module goatools.gosubdag.go_tasks) fill_relationshiprevgo2obj() (goatools.gosubdag.go_tasks.RelationshipFill method) fill_taxid2asscs() (goatools.anno.genetogo_reader.Gene2GoReader static method) FisherFactory (class in goatools.pvalcalc) FisherScipyStats (class in goatools.pvalcalc) fld2col_widths (goatools.gosubdag.rpt.wr_xlsx.GoSubDagWr attribute) (goatools.parsers.david_chart.DavidChartReader attribute) fld2prtfmt (goatools.parsers.david_chart.DavidChartReader attribute) flds (goatools.anno.init.reader_genetogo.InitAssc attribute) (goatools.anno.init.reader_idtogos.InitAssc attribute) fmt (goatools.statsdescribe.StatsDescribe attribute) fmt_dashes (goatools.rpt.write_hierarchy_base.WrHierPrt attribute) fmterr (goatools.pvalcalc.FisherScipyStats attribute) fmthdr (goatools.godag_plot.GODagPltVars attribute) fmtres (goatools.godag_plot.GODagPltVars attribute) (goatools.gosubdag.plot.goea_results.GoeaResults attribute) fmtsum (goatools.grouper.grprobj.Grouper attribute) fold_enrichment (goatools.go_enrichment.GOEnrichmentRecord property) ftp_get() (in module goatools.base) ftp_pub (goatools.anno.dnld_ebi_goa.DnldGoa attribute) G gaf_columns (goatools.anno.init.reader_gaf.GafData attribute) gaf_req_str (goatools.anno.init.reader_gaf.GafData attribute) gaf_req_str_2_2 (goatools.anno.init.reader_gaf.GafData attribute) gaf_required_columns (goatools.anno.init.reader_gaf.GafData attribute) GafData (class in goatools.anno.init.reader_gaf) GafHdr (class in goatools.anno.init.reader_gaf) gafhdr (goatools.anno.init.reader_gaf.GafData attribute) gafhdr2 (goatools.anno.init.reader_gaf.GafData attribute) gafhdr_ext (goatools.anno.init.reader_gaf.GafData attribute) GafReader (class in goatools.anno.gaf_reader) Gene2GoReader (class in goatools.anno.genetogo_reader) get_adj_records() (goatools.godag.prtfncs.GoeaPrintFunctions static method) get_algorithm() (in module goatools.goea.algorithms) get_all_child_edges() (goatools.obo_parser.GOTerm method) get_all_children() (goatools.obo_parser.GOTerm method) get_all_edge_nodes() (goatools.gosubdag.go_edges.EdgesBase method) get_all_lower() (goatools.obo_parser.GOTerm method) get_all_parent_edges() (goatools.obo_parser.GOTerm method) get_all_parents() (goatools.obo_parser.GOTerm method) (in module goatools.obo_tasks) get_all_upper() (goatools.obo_parser.GOTerm method) get_anno_desc() (in module goatools.anno.factory) get_annotations_reversed() (goatools.semantic.TermCounts method) get_assc_pruned() (in module goatools.associations) get_assoc() (goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS method) get_assoc_ncbi_taxids() (in module goatools.associations) get_associations() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_b2aset() (in module goatools.associations) (in module goatools.utils) get_basename() (goatools.anno.dnld_ebi_goa.DnldGoa method) get_bordercolor() (goatools.gosubdag.plot.go2color.Go2Color method) (goatools.grouper.colors.GrouperColors method) get_c2ps() (goatools.gosubdag.go_edges.EdgesBase method) get_child_objs() (in module goatools.gosubdag.go_tasks) get_chr2idx() (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll method) get_cnts_levels_depths_recs() (goatools.rpt.rpt_lev_depth.RptLevDepth static method) get_col_hdr() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) get_count() (goatools.semantic.TermCounts method) get_d1nts() (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr method) get_d1str() (goatools.gosubdag.godag_rcnt.CountRelatives method) get_data() (goatools.rpt.rpt_lev_depth.RptLevDepth method) get_date_yyyymmdd() (in module goatools.anno.init.utils) get_dbid2goids() (goatools.anno.annoreader_base.AnnoReaderBase method) get_deepest_common_ancestors() (in module goatools.semantic) get_depth2goobjs() (goatools.gosubdag.godag_rcnt_init.CountRelativesInit static method) get_desc() (goatools.anno.annoreader_base.AnnoReaderBase method) get_desc2nts() (goatools.grouper.sorter.Sorter method) get_desc2nts_fnc() (goatools.grouper.sorter.Sorter method) get_dfltdict() (goatools.anno.init.reader_gaf.GafData static method) get_dict_w_id2nts() (in module goatools.nt_utils) get_docargs() (goatools.cli.docopt_parse.DocOptParse method) (goatools.cli.gosubdag_plot.PlotCli method) get_dotstr() (goatools.grouper.plotobj.GoSubDagPlotNt method) get_edges() (goatools.godag_small.GODagSmall method) (goatools.gosubdag.go_edges.EdgesPath method) get_edgesobj() (in module goatools.gosubdag.go_edges) get_evcodes() (goatools.evidence_codes.EvidenceCodes method) get_evcodes_all() (goatools.evidence_codes.EvidenceCodes method) get_extensions() (in module goatools.anno.extensions.factory) get_field_values() (goatools.go_enrichment.GOEnrichmentRecord method) get_fieldname() (goatools.multiple_testing.Methods method) get_fields() (goatools.grouper.sorter.Sorter static method) get_fld2val() (goatools.statsdescribe.StatsDescribe method) get_fldnm_method() (goatools.multiple_testing.Methods static method) get_fmt_section() (goatools.wr_tbl_class.WbFmt method) get_fmtflds() (in module goatools.wr_tbl) get_fmtfldsdict() (in module goatools.wr_tbl) get_fncsortnt() (goatools.gosubdag.gosubdag.GoSubDag method) get_fout_base() (goatools.grouper.grprobj.Grouper method) get_fouts() (goatools.cli.wr_hierarchy.WrHierCli method) get_fragment() (in module goatools.godag.obographs) get_freq_msca() (in module goatools.semantic) get_gaf_hdr() (in module goatools.associations) get_gafvals() (goatools.anno.init.reader_gaf.GafData method) get_gene2binvec() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) get_go2ancestors() (in module goatools.godag.go_tasks) get_go2children() (in module goatools.godag.go_tasks) get_go2children_go2obj() (in module goatools.gosubdag.go_tasks) get_go2children_isa() (in module goatools.godag.go_tasks) get_go2color() (in module goatools.cli.gos_get) get_go2color_inst() (goatools.grouper.plotobj.PltGroupedGosArgs method) get_go2color_users() (goatools.grouper.colors.GrouperColors method) get_go2depth() (in module goatools.godag.go_tasks) get_go2descendants() (in module goatools.godag.go_tasks) get_go2nt() (goatools.gosubdag.gosubdag.GoSubDag method) (goatools.grouper.grprobj_init.GrouperInit method) get_go2nt_all() (goatools.gosubdag.gosubdag_init.InitFields method) get_go2obj() (goatools.cli.gos_get.GetGOs method) (goatools.gosubdag.gosubdag.GoSubDag method) get_go2obj_unique() (in module goatools.gosubdag.go_tasks) get_go2parents() (in module goatools.godag.go_tasks) get_go2parents_go2obj() (in module goatools.gosubdag.go_tasks) get_go2parents_isa() (in module goatools.godag.go_tasks) get_go2reldepth() (in module goatools.godag.reldepth) get_go2reldepth_main() (goatools.godag.reldepth.RelDepthCalc method) get_go2sectiontxt() (goatools.grouper.grprobj.Grouper method) get_go2txt() (goatools.grouper.grprplt.GrouperPlot static method) get_go_color() (goatools.cli.gosubdag_plot.CliGetGOs method) get_goargs() (goatools.cli.gos_get.GetGOs static method) get_godag() (in module goatools.base) get_goea_nts_all() (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs method) get_goea_nts_prt() (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs method) (in module goatools.rpt.goea_nt_xfrm) get_goid2color_pval() (goatools.gosubdag.plot.goea_results.GoeaResults method) get_goid2dbids() (goatools.anno.annoreader_base.AnnoReaderBase static method) get_goid_high() (goatools.grouper.grprobj_init.GrouperInit.GetGoidHigh method) get_goids() (goatools.cli.gos_get.GetGOs method) get_goids_all() (goatools.gosubdag.rpt.write_hierarchy.WrHierGO static method) get_goids_plt() (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot method) get_goids_sections() (goatools.gosubdag.rpt.wr_xlsx.GoSubDagWr static method) get_goids_to_remove() (in module goatools.anno.update_association) get_goobjs_altgo2goobj() (in module goatools.gosubdag.go_tasks) get_goone2ntletter() (goatools.gosubdag.godag_rcnt_init.CountRelativesInit method) get_gos_all() (goatools.grouper.grprobj_init.GrouperInit method) get_gos_d0d1() (goatools.grouper.grprdflts.GrouperDflts method) get_gosubdag() (goatools.grouper.grprdflts.GrouperDflts static method) get_gosubdag_all() (goatools.semantic.TermCounts method) get_gosubdagplot() (goatools.cli.gosubdag_plot.PlotCli method) (goatools.grouper.grprplt.GrouperPlot method) get_goterms_lower() (goatools.obo_parser.GOTerm method) get_goterms_lower_rels() (goatools.obo_parser.GOTerm method) get_goterms_upper() (goatools.obo_parser.GOTerm method) get_goterms_upper_rels() (goatools.obo_parser.GOTerm method) get_grp_name() (goatools.evidence_codes.EvidenceCodes method) get_h2i() (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) get_hdr() (goatools.anno.init.reader_gaf.GafHdr method) (goatools.anno.init.reader_gpad.GpadHdr method) (goatools.gosubdag.plot.go_node.GoNode method) get_hdrgo2usrgos() (goatools.grouper.grprobj.Grouper method) get_hdrgos() (goatools.grouper.grprobj.Grouper method) (goatools.grouper.hdrgos.HdrgosSections method) get_hdrgos_g_usrgos() (goatools.grouper.grprobj.Grouper method) get_hdrgos_u0() (goatools.grouper.grprobj.Grouper method) get_hdrgos_u1() (goatools.grouper.grprobj.Grouper method) get_hdrgos_unplaced() (goatools.grouper.grprobj.Grouper method) get_hdridx_flds() (in module goatools.grouper.utils) get_hdrs() (goatools.wr_tbl_class.WbFmt method) (in module goatools.wr_tbl_class) get_id2children() (in module goatools.godag.go_tasks) get_id2gos() (goatools.anno.annoreader_base.AnnoReaderBase method) get_id2gos_all() (goatools.anno.genetogo_reader.Gene2GoReader static method) get_id2gos_nss() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_id2lower() (in module goatools.godag.go_tasks) get_id2lowerselect() (in module goatools.godag.go_tasks) get_id2obj_cur_n_high() (goatools.godag.go_tasks.CurNHigher method) get_id2parents() (in module goatools.godag.go_tasks) get_id2upper() (in module goatools.godag.go_tasks) get_id2upperselect() (in module goatools.godag.go_tasks) get_indent_dots() (goatools.go_enrichment.GOEnrichmentRecord method) get_info_content() (in module goatools.semantic) get_item_cnt() (goatools.go_enrichment.GOEnrichmentStudy static method) get_items() (goatools.go_search.GoSearch method) get_key_goids() (goatools.gosubdag.gosubdag.GoSubDag method) get_kwargs() (in module goatools.gosubdag.utils) get_kwargs_set() (in module goatools.gosubdag.utils) get_kws() (goatools.gosubdag.plot.go_edge.GoEdgeOpts method) (goatools.gosubdag.plot.go_node.GoNodeOpts method) get_kws_plt() (goatools.grouper.plotobj.PltGroupedGosArgs method) get_leaf_children() (in module goatools.gosubdag.go_tasks) get_lines() (in module goatools.wr_tbl) get_list_w_id2nts() (in module goatools.nt_utils) get_logger() (in module goatools.base) get_matching_gos() (goatools.go_search.GoSearch method) get_method_name() (goatools.go_enrichment.GOEnrichmentRecord method) get_min_inc_exc() (goatools.evidence_codes.EvidenceCodes method) get_most_specific_dcnt() (in module goatools.gosubdag.go_most_specific) get_most_specific_tinfo() (in module goatools.gosubdag.go_most_specific) get_most_specific_tinfo_dcnt() (in module goatools.gosubdag.go_most_specific) get_name() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_node() (goatools.gosubdag.plot.go_node.GoNode method) get_node_text() (goatools.gosubdag.plot.go_node.GoNode method) get_ns2assc() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_ns2goids() (goatools.gosubdag.gosubdag.GoSubDag method) get_ns2nts() (goatools.go_enrichment.GOEnrichmentStudy static method) get_ns2ntsanno() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_nt() (goatools.grouper.grprobj_init.GrouperInit.NtMaker method) get_ntgos_sorted() (goatools.grouper.wr_sections.WrSectionsBase method) get_ntobj() (goatools.anno.init.reader_gaf.GafData method) (goatools.rpt.nts_xfrm.MgrNts method) get_nts() (goatools.gosubdag.gosubdag.GoSubDag method) (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) get_nts_flat() (goatools.grouper.sorter.Sorter method) get_nts_sections() (goatools.gosubdag.rpt.wr_xlsx.GoSubDagWr method) get_nts_sorted() (goatools.grouper.sorter_gos.SorterGoIds method) get_nts_strpval() (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs method) get_num_sig() (goatools.parsers.david_chart.DavidChartReader method) get_objanno() (in module goatools.anno.factory) get_objanno_g_kws() (in module goatools.anno.factory) get_objgrpwr() (goatools.cli.find_enrichment.GroupItems method) get_obo_id() (in module goatools.godag.obographs) get_optional_attrs() (goatools.godag.obo_optional_attributes.OboOptionalAttrs static method) get_order() (goatools.evidence_codes.EvidenceCodes method) get_outfile() (goatools.cli.gosubdag_plot.PlotCli method) get_overlap() (goatools.cli.find_enrichment.GoeaCliFnc static method) get_parents_letters() (goatools.gosubdag.godag_rcnt.CountRelatives method) get_paths_from_to() (goatools.gosubdag.go_paths.GoPaths method) get_paths_goobjs() (in module goatools.gosubdag.go_paths) get_pltdotstr() (goatools.grouper.grprplt.GrouperPlot method) get_pltdotstrs() (goatools.grouper.grprplt.GrouperPlot method) (goatools.grouper.plotobj.PltGroupedGos method) get_pltpat() (goatools.grouper.plotobj.GoSubDagPlotNt method) get_present() (goatools.gosubdag.plot.go_node.GoNodeOpts method) get_prt_flds() (goatools.wr_tbl_class.WbFmt method) get_prt_fmt() (goatools.gosubdag.gosubdag_init.InitFields method) get_prt_hdr() (goatools.gosubdag.gosubdag_init.InitFields method) get_prtflds_all() (goatools.go_enrichment.GOEnrichmentRecord method) get_prtflds_default() (goatools.go_enrichment.GOEnrichmentRecord method) (goatools.godag.prtfncs.GoeaPrintFunctions static method) get_prtfmt() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) get_prtfmt_list() (goatools.rpt.prtfmt.PrtFmt method) get_prtfmt_str() (goatools.rpt.prtfmt.PrtFmt method) get_pval_field() (goatools.cli.find_enrichment.GoeaCliFnc method) get_pval_uncorr() (goatools.go_enrichment.GOEnrichmentStudy method) get_pvalue() (goatools.go_enrichment.GOEnrichmentRecord method) get_pydot_graph() (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot method) get_rcntobj() (goatools.gosubdag.gosubdag_init.InitFields method) get_relation_cnt() (goatools.anno.gpad_reader.GpadReader method) get_relations_cnt() (goatools.anno.extensions.extensions.AnnotationExtensions method) get_relationship_combos() (goatools.godag.relationship_combos.RelationshipCombos method) get_relationship_targets() (in module goatools.godag.go_tasks) get_results() (goatools.cli.find_enrichment.GoeaCliFnc method) get_results_msg() (goatools.go_enrichment.GOEnrichmentStudy method) get_results_sig() (goatools.cli.find_enrichment.GoeaCliFnc method) get_section2items() (goatools.grouper.grprobj.Grouper method) get_section2usrnts() (goatools.grouper.grprobj.Grouper method) get_section_hdrgos() (goatools.grouper.hdrgos.HdrgosSections method) get_section_hdrgos_nts() (goatools.grouper.grprobj.Grouper method) get_section_marks() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) get_sections() (goatools.grouper.hdrgos.HdrgosSections method) get_sections_2d() (goatools.grouper.grprobj.Grouper method) get_sections_2d_nts() (goatools.grouper.grprobj.Grouper method) get_sections_2dnt() (goatools.grouper.wr_sections.WrSectionsBase method) get_sections_flattened() (goatools.grouper.sorter.Sorter static method) get_seed_hexstr() (goatools.randseed.RandomSeed32 method) get_seed_str() (goatools.randseed.RandomSeed32 static method) get_set() (goatools.godag.relationship_combos.RelationshipCombos method) (goatools.rpt.nts_xfrm.MgrNts method) get_short_plot_name() (in module goatools.gosubdag.plot.go_name_shorten) get_sim() (goatools.semsim.termwise.wang.SsWang method) get_sorted_hdrgo2usrgos() (goatools.grouper.sorter_gos.SorterGoIds method) get_sorted_nts_keep_section() (goatools.grouper.sorter_nts.SorterNts method) get_sorted_nts_omit_section() (goatools.grouper.sorter_nts.SorterNts method) get_sorted_relationship() (in module goatools.gosubdag.go_tasks) get_sortobj() (goatools.cli.find_enrichment.GroupItems method) get_statsmodels_multipletests() (goatools.multiple_testing.Methods method) get_study_items() (goatools.go_enrichment.GOEnrichmentStudy static method) (goatools.rpt.goea_nt_xfrm.MgrNtGOEAs method) (in module goatools.rpt.goea_nt_xfrm) get_study_txt() (goatools.gosubdag.plot.goea_results.GoeaResults method) get_summary_data() (goatools.grouper.wr_sections.WrSectionsBase method) get_summary_str() (goatools.grouper.wr_sections.WrSectionsBase method) get_sv() (goatools.semsim.termwise.dag_a.DagA method) get_svalues() (goatools.semsim.termwise.dag_a.DagA method) get_taxid() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) get_taxid2asscs() (goatools.anno.genetogo_reader.Gene2GoReader method) get_tcntobj() (in module goatools.associations) get_term_freq() (goatools.semantic.TermCounts method) get_terms() (in module goatools.ratio) get_total_count() (goatools.semantic.TermCounts method) get_type_filename() (in module goatools.anno.factory) get_unique_fields() (in module goatools.nt_utils) get_usrgo2hdrgo() (goatools.grouper.grprobj.Grouper method) get_usrgo2sections() (goatools.grouper.grprobj.Grouper method) get_usrgos() (goatools.cli.gos_get.GetGOs method) get_usrgos_g_hdrgos() (goatools.grouper.grprobj.Grouper method) get_usrgos_g_section() (goatools.grouper.grprobj.Grouper method) get_usrgos_w_parents() (goatools.grouper.grprobj.Grouper method) get_vals() (goatools.gosubdag.gosubdag.GoSubDag method) get_wbfmt() (goatools.wr_tbl_class.WbFmt method) getfnc_qual_ev() (goatools.anno.opts.AnnoOptions method) GetGOs (class in goatools.cli.gos_get) getmsg_valid_methods() (goatools.multiple_testing.Methods method) getstr_data() (goatools.statsdescribe.StatsDescribe method) Go2Color (class in goatools.gosubdag.plot.go2color) go2flds (goatools.goea.algorithms.base.GoeaAlgoResult attribute) (goatools.goea.algorithms.GoeaAlgoResult attribute) go2popitems (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) go2pval (goatools.goea.algorithms.base.GoeaAlgoResult attribute) (goatools.goea.algorithms.GoeaAlgoResult attribute) go2studyitems (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) goatools module goatools.anno module goatools.anno.annoreader_base module goatools.anno.broad_gos module goatools.anno.dnld_ebi_goa module goatools.anno.eco2group module goatools.anno.extensions module goatools.anno.extensions.extension module goatools.anno.extensions.extensions module goatools.anno.extensions.factory module goatools.anno.factory module goatools.anno.gaf_reader module goatools.anno.genetogo_reader module goatools.anno.gpad_reader module goatools.anno.idtogos_reader module goatools.anno.init module goatools.anno.init.reader_gaf module goatools.anno.init.reader_genetogo module goatools.anno.init.reader_gpad module goatools.anno.init.reader_idtogos module goatools.anno.init.utils module goatools.anno.opts module goatools.anno.update_association module goatools.associations module goatools.base module goatools.cli module goatools.cli.compare_gos module goatools.cli.docopt_parse module goatools.cli.fetch_associations module goatools.cli.find_enrichment module goatools.cli.gos_get module goatools.cli.gosubdag_plot module goatools.cli.grouped module goatools.cli.main module goatools.cli.map_to_slim module goatools.cli.ncbi_gene_results_to_python module goatools.cli.plot_go_term module goatools.cli.prt_terms module goatools.cli.wr_hierarchy module goatools.cli.wr_sections module goatools.evidence_codes module goatools.go_enrichment module goatools.go_search module goatools.godag module goatools.godag.consts module goatools.godag.go_tasks module goatools.godag.obo_optional_attributes module goatools.godag.obographs module goatools.godag.prtfncs module goatools.godag.prttime module goatools.godag.relationship_combos module goatools.godag.relationship_str module goatools.godag.reldepth module goatools.godag.typedef module goatools.godag_obosm module goatools.godag_plot module goatools.godag_small module goatools.goea module goatools.goea.algorithms module goatools.goea.algorithms.base module goatools.goea.algorithms.classic module goatools.goea.algorithms.elim module goatools.goea.go_enrichment_ns module goatools.gosubdag module goatools.gosubdag.go_edges module goatools.gosubdag.go_most_specific module goatools.gosubdag.go_paths module goatools.gosubdag.go_tasks module goatools.gosubdag.godag_rcnt module goatools.gosubdag.godag_rcnt_init module goatools.gosubdag.gosubdag module goatools.gosubdag.gosubdag_init module goatools.gosubdag.plot module goatools.gosubdag.plot.go2color module goatools.gosubdag.plot.go_edge module goatools.gosubdag.plot.go_name_shorten module goatools.gosubdag.plot.go_node module goatools.gosubdag.plot.goea_results module goatools.gosubdag.plot.gosubdag_plot module goatools.gosubdag.plot.plot module goatools.gosubdag.rpt module goatools.gosubdag.rpt.wr_xlsx module goatools.gosubdag.rpt.write_hierarchy module goatools.gosubdag.utils module goatools.grouper module goatools.grouper.aart_geneproducts_all module goatools.grouper.aart_geneproducts_one module goatools.grouper.colors module goatools.grouper.grprdflts module goatools.grouper.grprobj module goatools.grouper.grprobj_init module goatools.grouper.grprplt module goatools.grouper.hdrgos module goatools.grouper.plotobj module goatools.grouper.read_goids module goatools.grouper.sorter module goatools.grouper.sorter_gos module goatools.grouper.sorter_nts module goatools.grouper.tasks module goatools.grouper.utils module goatools.grouper.wr_sections module goatools.grouper.wrxlsx module goatools.mapslim module goatools.multiple_testing module goatools.nt_utils module goatools.obo_parser module goatools.obo_tasks module goatools.parsers module goatools.parsers.david_chart module goatools.parsers.ncbi_gene_file_reader module goatools.pvalcalc module goatools.randseed module goatools.ratio module goatools.rpt module goatools.rpt.goea_nt_xfrm module goatools.rpt.nts_xfrm module goatools.rpt.prtfmt module goatools.rpt.rpt_lev_depth module goatools.rpt.write_hierarchy_base module goatools.semantic module goatools.semsim module goatools.semsim.termwise module goatools.semsim.termwise.dag_a module goatools.semsim.termwise.wang module goatools.statsdescribe module goatools.utils module goatools.version module goatools.wr_tbl module goatools.wr_tbl_class module GODag (class in goatools.obo_parser) godag (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) GODagPltVars (class in goatools.godag_plot) GODagSmall (class in goatools.godag_small) GODagSmallPlot (class in goatools.godag_plot) GoDagTimed (class in goatools.godag.prttime) GoDepth1LettersWr (class in goatools.gosubdag.rpt.wr_xlsx) GoeaAlgoResult (class in goatools.goea.algorithms) (class in goatools.goea.algorithms.base) GoeaAlgorithm (class in goatools.goea.algorithms) (class in goatools.goea.algorithms.base) GoeaCliArgs (class in goatools.cli.find_enrichment) GoeaCliFnc (class in goatools.cli.find_enrichment) GoeaContext (class in goatools.goea.algorithms) (class in goatools.goea.algorithms.base) GoeaPrintFunctions (class in goatools.godag.prtfncs) GoeaResults (class in goatools.gosubdag.plot.goea_results) GoEdge (class in goatools.gosubdag.plot.go_edge) GoEdgeOpts (class in goatools.gosubdag.plot.go_edge) GOEnrichmentRecord (class in goatools.go_enrichment) GOEnrichmentStudy (class in goatools.go_enrichment) GOEnrichmentStudyNS (class in goatools.goea.go_enrichment_ns) goid_is_valid() (in module goatools.gosubdag.go_tasks) goids (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) goids_valid() (in module goatools.gosubdag.go_tasks) GoNode (class in goatools.gosubdag.plot.go_node) GoNodeOpts (class in goatools.gosubdag.plot.go_node) GoPaths (class in goatools.gosubdag.go_paths) GoSearch (class in goatools.go_search) GoSubDag (class in goatools.gosubdag.gosubdag) GoSubDagPlot (class in goatools.gosubdag.plot.gosubdag_plot) GoSubDagPlotNt (class in goatools.grouper.plotobj) GoSubDagWr (class in goatools.gosubdag.rpt.wr_xlsx) GOTerm (class in goatools.obo_parser) GpadHdr (class in goatools.anno.init.reader_gpad) gpadhdr (goatools.anno.init.reader_gpad.InitAssc attribute) GpadReader (class in goatools.anno.gpad_reader) Grouped (class in goatools.cli.grouped) Grouper (class in goatools.grouper.grprobj) GrouperColors (class in goatools.grouper.colors) GrouperDflts (class in goatools.grouper.grprdflts) GrouperInit (class in goatools.grouper.grprobj_init) GrouperInit.GetGoidHigh (class in goatools.grouper.grprobj_init) GrouperInit.NtMaker (class in goatools.grouper.grprobj_init) GrouperPlot (class in goatools.grouper.grprplt) GroupItems (class in goatools.cli.find_enrichment) GrpWr (class in goatools.cli.find_enrichment) gunzip() (in module goatools.base) gzip_open_to() (in module goatools.base) H has_child() (goatools.obo_parser.GOTerm method) has_ns() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.gaf_reader.GafReader method) (goatools.anno.genetogo_reader.Gene2GoReader method) has_parent() (goatools.obo_parser.GOTerm method) hdr_xform() (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) hdrcol_all (goatools.grouper.colors.GrouperColors attribute) hdrgo_dflt_color (goatools.grouper.plotobj.PltGroupedGosArgs attribute) HdrgosSections (class in goatools.grouper.hdrgos) hdrs (goatools.anno.init.reader_genetogo.InitAssc attribute) (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr attribute) hms() (goatools.anno.annoreader_base.AnnoReaderBase method) HolmBonferroni (class in goatools.multiple_testing) http_get() (in module goatools.base) I id2int() (goatools.obo_parser.GODag static method) IdToGosReader (class in goatools.anno.idtogos_reader) IdToLowerSelect (class in goatools.godag.go_tasks) IdToUpperSelect (class in goatools.godag.go_tasks) incexc2num (goatools.anno.opts.AnnoOptions attribute) init_associations() (goatools.anno.init.reader_gaf.InitAssc method) (goatools.anno.init.reader_genetogo.InitAssc method) (goatools.anno.init.reader_gpad.InitAssc method) (goatools.anno.init.reader_idtogos.InitAssc method) init_datamembers() (goatools.godag.obo_optional_attributes.OboOptionalAttrs method) init_dicts() (goatools.rpt.nts_xfrm.MgrNts method) init_goid2color() (goatools.gosubdag.plot.go2color.Go2Color method) init_goids() (goatools.cli.wr_hierarchy.WrHierCli static method) InitAssc (class in goatools.anno.init.reader_gaf) (class in goatools.anno.init.reader_genetogo) (class in goatools.anno.init.reader_gpad) (class in goatools.anno.init.reader_idtogos) InitFields (class in goatools.gosubdag.gosubdag_init) InitGOs (class in goatools.gosubdag.gosubdag_init) internal_get_goids_or_sections() (goatools.grouper.read_goids.ReadGoids method) is_ratio_different() (in module goatools.ratio) items_p_line (goatools.godag_plot.GODagPltVars attribute) K key2col (goatools.godag_plot.GODagPltVars attribute) (goatools.gosubdag.plot.go2color.Go2Color attribute) keys_exp (goatools.anno.opts.AnnoOptions attribute) (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll attribute) keys_loc (goatools.grouper.plotobj.PltGroupedGosArgs attribute) keys_nts (goatools.grouper.sorter.Sorter attribute) keys_plt (goatools.grouper.plotobj.PltGroupedGosArgs attribute) kw_keys_xlsx (goatools.grouper.wrxlsx.WrXlsxSortedGos attribute) kws_all (goatools.gosubdag.rpt.write_hierarchy.WrHierGO attribute) kws_aux_gos (goatools.gosubdag.gosubdag_init.InitGOs attribute) kws_dct (goatools.gosubdag.plot.go2color.Go2Color attribute) (goatools.gosubdag.rpt.write_hierarchy.WrHierGO attribute) kws_dct_all (goatools.cli.wr_hierarchy.WrHierCli attribute) kws_dct_wr (goatools.cli.wr_hierarchy.WrHierCli attribute) kws_dict (goatools.cli.compare_gos.CompareGOsCli attribute) (goatools.cli.gosubdag_plot.PlotCli attribute) (goatools.cli.grouped.Grouped attribute) (goatools.cli.prt_terms.PrtGOterms attribute) (goatools.cli.wr_sections.WrSectionsCli attribute) kws_ok (goatools.go_enrichment.GOEnrichmentStudy attribute) (goatools.gosubdag.gosubdag.GoSubDag attribute) kws_plt (goatools.cli.gosubdag_plot.PlotCli attribute) kws_set (goatools.cli.compare_gos.CompareGOsCli attribute) (goatools.cli.gosubdag_plot.PlotCli attribute) (goatools.cli.prt_terms.PrtGOterms attribute) (goatools.cli.wr_sections.WrSectionsCli attribute) (goatools.gosubdag.plot.goea_results.GoeaResults attribute) (goatools.gosubdag.rpt.write_hierarchy.WrHierGO attribute) kws_set_all (goatools.cli.wr_hierarchy.WrHierCli attribute) L label_wrap() (goatools.obo_parser.GODag method) lin_sim() (in module goatools.semantic) lin_sim_calc() (in module goatools.semantic) load_dag() (goatools.godag.prttime.GoDagTimed method) load_obo_file() (goatools.obo_parser.GODag method) log (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) M main() (in module goatools.cli.compare_gos) (in module goatools.cli.fetch_associations) (in module goatools.cli.find_enrichment) (in module goatools.cli.gosubdag_plot) (in module goatools.cli.main) (in module goatools.cli.map_to_slim) (in module goatools.cli.ncbi_gene_results_to_python) (in module goatools.cli.plot_go_term) (in module goatools.cli.prt_terms) (in module goatools.cli.wr_hierarchy) (in module goatools.cli.wr_sections) make_graph_pydot() (goatools.obo_parser.GODag method) make_graph_pygraphviz() (goatools.obo_parser.GODag method) mapslim() (in module goatools.mapslim) max_gos (goatools.cli.gosubdag_plot.CliGetGOs attribute) mcorrection_factory() (in module goatools.multiple_testing) method (goatools.multiple_testing.Methods.NtMethodInfo attribute) Methods (class in goatools.multiple_testing) Methods.NtMethodInfo (class in goatools.multiple_testing) MgrNtGOEAs (class in goatools.rpt.goea_nt_xfrm) MgrNts (class in goatools.rpt.nts_xfrm) min_branch_length() (in module goatools.semantic) mk_fmtfld() (in module goatools.wr_tbl) mknts() (goatools.rpt.nts_xfrm.MgrNts method) module goatools goatools.anno goatools.anno.annoreader_base goatools.anno.broad_gos goatools.anno.dnld_ebi_goa goatools.anno.eco2group goatools.anno.extensions goatools.anno.extensions.extension goatools.anno.extensions.extensions goatools.anno.extensions.factory goatools.anno.factory goatools.anno.gaf_reader goatools.anno.genetogo_reader goatools.anno.gpad_reader goatools.anno.idtogos_reader goatools.anno.init goatools.anno.init.reader_gaf goatools.anno.init.reader_genetogo goatools.anno.init.reader_gpad goatools.anno.init.reader_idtogos goatools.anno.init.utils goatools.anno.opts goatools.anno.update_association goatools.associations goatools.base goatools.cli goatools.cli.compare_gos goatools.cli.docopt_parse goatools.cli.fetch_associations goatools.cli.find_enrichment goatools.cli.gos_get goatools.cli.gosubdag_plot goatools.cli.grouped goatools.cli.main goatools.cli.map_to_slim goatools.cli.ncbi_gene_results_to_python goatools.cli.plot_go_term goatools.cli.prt_terms goatools.cli.wr_hierarchy goatools.cli.wr_sections goatools.evidence_codes goatools.go_enrichment goatools.go_search goatools.godag goatools.godag.consts goatools.godag.go_tasks goatools.godag.obo_optional_attributes goatools.godag.obographs goatools.godag.prtfncs goatools.godag.prttime goatools.godag.relationship_combos goatools.godag.relationship_str goatools.godag.reldepth goatools.godag.typedef goatools.godag_obosm goatools.godag_plot goatools.godag_small goatools.goea goatools.goea.algorithms goatools.goea.algorithms.base goatools.goea.algorithms.classic goatools.goea.algorithms.elim goatools.goea.go_enrichment_ns goatools.gosubdag goatools.gosubdag.go_edges goatools.gosubdag.go_most_specific goatools.gosubdag.go_paths goatools.gosubdag.go_tasks goatools.gosubdag.godag_rcnt goatools.gosubdag.godag_rcnt_init goatools.gosubdag.gosubdag goatools.gosubdag.gosubdag_init goatools.gosubdag.plot goatools.gosubdag.plot.go2color goatools.gosubdag.plot.go_edge goatools.gosubdag.plot.go_name_shorten goatools.gosubdag.plot.go_node goatools.gosubdag.plot.goea_results goatools.gosubdag.plot.gosubdag_plot goatools.gosubdag.plot.plot goatools.gosubdag.rpt goatools.gosubdag.rpt.wr_xlsx goatools.gosubdag.rpt.write_hierarchy goatools.gosubdag.utils goatools.grouper goatools.grouper.aart_geneproducts_all goatools.grouper.aart_geneproducts_one goatools.grouper.colors goatools.grouper.grprdflts goatools.grouper.grprobj goatools.grouper.grprobj_init goatools.grouper.grprplt goatools.grouper.hdrgos goatools.grouper.plotobj goatools.grouper.read_goids goatools.grouper.sorter goatools.grouper.sorter_gos goatools.grouper.sorter_nts goatools.grouper.tasks goatools.grouper.utils goatools.grouper.wr_sections goatools.grouper.wrxlsx goatools.mapslim goatools.multiple_testing goatools.nt_utils goatools.obo_parser goatools.obo_tasks goatools.parsers goatools.parsers.david_chart goatools.parsers.ncbi_gene_file_reader goatools.pvalcalc goatools.randseed goatools.ratio goatools.rpt goatools.rpt.goea_nt_xfrm goatools.rpt.nts_xfrm goatools.rpt.prtfmt goatools.rpt.rpt_lev_depth goatools.rpt.write_hierarchy_base goatools.semantic goatools.semsim goatools.semsim.termwise goatools.semsim.termwise.dag_a goatools.semsim.termwise.wang goatools.statsdescribe goatools.utils goatools.version goatools.wr_tbl goatools.wr_tbl_class most_informative_common_ancestor() (in module goatools.semantic) most_specific_fncs (goatools.grouper.grprobj_init.GrouperInit attribute) N name (goatools.goea.algorithms.base.GoeaAlgorithm attribute) (goatools.goea.algorithms.classic.ClassicAlgorithm attribute) (goatools.goea.algorithms.ClassicAlgorithm attribute) (goatools.goea.algorithms.elim.ElimAlgorithm attribute) (goatools.goea.algorithms.ElimAlgorithm attribute) (goatools.goea.algorithms.GoeaAlgorithm attribute) namespace2NS (goatools.go_enrichment.GOEnrichmentRecord attribute) ncbi_tsv_to_py() (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli method) (in module goatools.cli.ncbi_gene_results_to_python) NCBIgeneFileReader (class in goatools.parsers.ncbi_gene_file_reader) NCBIgeneToPythonCli (class in goatools.cli.ncbi_gene_results_to_python) nd_not2desc (goatools.anno.opts.AnnoOptions attribute) no_duplicates_sections2d() (in module goatools.grouper.utils) nopen() (in module goatools.base) nss (goatools.rpt.rpt_lev_depth.RptLevDepth attribute) ntobj (goatools.evidence_codes.EvidenceCodes attribute) (goatools.grouper.grprobj_init.GrouperInit.NtMaker attribute) ntpltgo (goatools.grouper.plotobj.PltGroupedGos attribute) nts_ev_nd() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.idtogos_reader.IdToGosReader method) nts_qual_not() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.idtogos_reader.IdToGosReader method) num_goterms() (goatools.godag_small.GODagSmall method) num_hdrgos() (goatools.grouper.hdrgos.HdrgosSections method) O objprtfmt (goatools.cli.find_enrichment.GrpWr attribute) objprtres (goatools.go_enrichment.GOEnrichmentStudy attribute) OboGraphsReader (class in goatools.godag.obographs) OboOptionalAttrs (class in goatools.godag.obo_optional_attributes) OBOReader (class in goatools.obo_parser) OboToGoDagSmall (class in goatools.godag_obosm) optional_exp (goatools.godag.obo_optional_attributes.OboOptionalAttrs attribute) options (goatools.pvalcalc.FisherFactory attribute) P path2edges() (in module goatools.gosubdag.go_paths) paths2edges() (in module goatools.gosubdag.go_paths) paths_to_top() (goatools.obo_parser.GODag method) plot() (goatools.cli.gosubdag_plot.PlotCli method) plot_goid2goobj() (in module goatools.godag_plot) plot_gos() (goatools.grouper.grprplt.GrouperPlot method) (in module goatools.godag_plot) (in module goatools.gosubdag.plot.plot) plot_grouped_gos() (goatools.grouper.grprplt.GrouperPlot method) plot_groups_all() (goatools.grouper.grprplt.GrouperPlot method) (goatools.grouper.plotobj.PltGroupedGos method) plot_groups_unplaced() (goatools.grouper.grprplt.GrouperPlot method) (goatools.grouper.plotobj.PltGroupedGos method) plot_results() (in module goatools.godag_plot) (in module goatools.gosubdag.plot.plot) plot_sections() (goatools.grouper.grprplt.GrouperPlot method) (goatools.grouper.plotobj.PltGroupedGos method) PlotCli (class in goatools.cli.gosubdag_plot) plt() (goatools.godag_plot.GODagSmallPlot method) plt_dag() (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot method) plt_goea_results() (in module goatools.godag_plot) (in module goatools.gosubdag.plot.plot) plt_goids() (in module goatools.gosubdag.plot.plot) PltGroupedGos (class in goatools.grouper.plotobj) PltGroupedGosArgs (class in goatools.grouper.plotobj) pop_n (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) prefixes (goatools.multiple_testing.Methods attribute) print_date() (goatools.godag.prtfncs.GoeaPrintFunctions static method) print_results() (goatools.go_enrichment.GOEnrichmentStudy method) (goatools.godag.prtfncs.GoeaPrintFunctions method) print_results_adj() (goatools.godag.prtfncs.GoeaPrintFunctions method) propagate_counts (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) prt() (goatools.randseed.RandomSeed32 method) prt_cfg() (goatools.semsim.termwise.wang.SsWang method) prt_col_hdr() (goatools.grouper.wr_sections.WrSectionsBase method) prt_counts() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.genetogo_reader.Gene2GoReader method) prt_data() (goatools.statsdescribe.StatsDescribe method) prt_details() (goatools.evidence_codes.EvidenceCodes method) prt_error_summary() (goatools.anno.init.reader_gaf.GafData method) prt_ev_cnts() (goatools.evidence_codes.EvidenceCodes method) prt_flds (goatools.parsers.david_chart.DavidChartReader attribute) prt_gene_aart() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_gene_aart_details() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_goid_cnt() (goatools.grouper.wr_sections.WrSectionsTxt method) prt_goids() (goatools.gosubdag.gosubdag.GoSubDag method) (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot method) prt_gos() (goatools.grouper.sorter.Sorter method) prt_gos_flat() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_gos_grouped() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_hdr() (goatools.statsdescribe.StatsDescribe method) prt_header() (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr static method) prt_hier() (goatools.cli.wr_hierarchy.WrHierCli method) prt_hier_all() (goatools.gosubdag.rpt.write_hierarchy.WrHierGO method) prt_hier_down() (goatools.gosubdag.rpt.write_hierarchy.WrHierGO method) prt_hier_rec() (goatools.rpt.write_hierarchy_base.WrHierPrt method) prt_hier_up() (goatools.gosubdag.rpt.write_hierarchy.WrHierGO method) prt_hms() (in module goatools.godag.prttime) prt_info() (goatools.grouper.wr_sections.WrSectionsTxt method) prt_keys() (goatools.godag.relationship_str.RelationshipStr method) prt_lev_depth() (in module goatools.rpt.rpt_lev_depth) prt_line_detail() (goatools.anno.init.reader_gaf.GafData method) prt_mdtbl() (goatools.parsers.david_chart.DavidChartReader method) prt_mrks() (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll method) prt_ntgos() (goatools.grouper.wr_sections.WrSectionsBase method) prt_nts() (goatools.grouper.sorter.Sorter method) (in module goatools.nt_utils) (in module goatools.wr_tbl) prt_num_sig() (goatools.parsers.david_chart.DavidChartReader method) prt_objdesc() (goatools.gosubdag.gosubdag.GoSubDag method) (goatools.semantic.TermCounts method) prt_outfiles_flat() (goatools.cli.find_enrichment.GoeaCliFnc method) prt_outfiles_grouped() (goatools.cli.find_enrichment.GrpWr method) prt_paths() (goatools.gosubdag.go_paths.GoPaths static method) prt_qualifiers() (goatools.anno.annoreader_base.AnnoReaderBase method) prt_report_grp0() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_report_grp1() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_results() (goatools.cli.find_enrichment.GoeaCliFnc method) prt_section_key() (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll method) (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) prt_sections() (goatools.grouper.wr_sections.WrSectionsTxt static method) prt_seed() (goatools.randseed.RandomSeed32 method) prt_summary() (goatools.gosubdag.plot.goea_results.GoeaResults method) (goatools.grouper.grprobj.Grouper method) prt_summary_anno2ev() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.idtogos_reader.IdToGosReader method) (goatools.evidence_codes.EvidenceCodes method) prt_summary_code() (goatools.evidence_codes.EvidenceCodes method) prt_tsv() (goatools.cli.find_enrichment.GrpWr method) (goatools.go_enrichment.GOEnrichmentStudy method) (in module goatools.wr_tbl) prt_tsv_dat() (in module goatools.wr_tbl) prt_tsv_hdr() (in module goatools.wr_tbl) prt_tsv_sections() (in module goatools.wr_tbl) prt_txt() (goatools.cli.find_enrichment.GrpWr method) (goatools.go_enrichment.GOEnrichmentStudy static method) (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr method) (in module goatools.wr_tbl) prt_txt_desc2nts() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) prt_ver() (goatools.grouper.wr_sections.WrSectionsBase method) PrtFmt (class in goatools.rpt.prtfmt) prtfmt_dflt (goatools.rpt.prtfmt.PrtFmt attribute) PrtGOterms (class in goatools.cli.prt_terms) prttex_summary_cnts_all() (goatools.rpt.rpt_lev_depth.RptLevDepth method) PvalCalcBase (class in goatools.pvalcalc) pvals_precorrected (goatools.goea.algorithms.base.GoeaAlgorithm attribute) (goatools.goea.algorithms.elim.ElimAlgorithm attribute) (goatools.goea.algorithms.ElimAlgorithm attribute) (goatools.goea.algorithms.GoeaAlgorithm attribute) Q query_term() (goatools.obo_parser.GODag method) R RandomSeed32 (class in goatools.randseed) rd_files() (goatools.cli.find_enrichment.GoeaCliFnc method) rdtxt_gos() (goatools.cli.gos_get.GetGOs static method) rdtxt_gos_color() (goatools.cli.gos_get.GetGOs static method) read_annotations() (in module goatools.associations) read_associations() (in module goatools.associations) read_d1_letter() (in module goatools.gosubdag.rpt.wr_xlsx) read_gaf() (goatools.anno.gaf_reader.GafReader method) (in module goatools.associations) read_geneset() (in module goatools.utils) read_goids() (in module goatools.grouper.read_goids) read_ncbi_gene2go() (in module goatools.associations) read_py() (goatools.grouper.read_goids.ReadGoids method) read_sections() (goatools.grouper.read_goids.ReadGoids method) (in module goatools.grouper.read_goids) read_txt() (goatools.grouper.read_goids.ReadGoids method) ReadGoids (class in goatools.grouper.read_goids) reduce_annotations() (goatools.anno.annoreader_base.AnnoReaderBase method) (goatools.anno.idtogos_reader.IdToGosReader method) rel2chr (goatools.godag.relationship_str.RelationshipStr attribute) rel2col (goatools.godag_plot.GODagPltVars attribute) rel2edgekws (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot attribute) relation2qualifier (goatools.anno.init.reader_gpad.InitAssc attribute) RelationshipCombos (class in goatools.godag.relationship_combos) RelationshipFill (class in goatools.gosubdag.go_tasks) relationships (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) RelationshipStr (class in goatools.godag.relationship_str) RelDepthCalc (class in goatools.godag.reldepth) remove_assc_goids() (in module goatools.anno.update_association) replace_greek() (in module goatools.gosubdag.plot.go_name_shorten) replace_greek_tex() (in module goatools.gosubdag.plot.go_name_shorten) replace_nulls() (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader static method) resnik_sim() (in module goatools.semantic) rev2chr (goatools.godag.relationship_str.RelationshipStr attribute) rm_gos() (goatools.gosubdag.go_edges.EdgesBase method) rpt_invalid_method() (goatools.multiple_testing.Methods method) RptLevDepth (class in goatools.rpt.rpt_lev_depth) run() (goatools.goea.algorithms.base.GoeaAlgorithm method) (goatools.goea.algorithms.classic.ClassicAlgorithm method) (goatools.goea.algorithms.ClassicAlgorithm method) (goatools.goea.algorithms.elim.ElimAlgorithm method) (goatools.goea.algorithms.ElimAlgorithm method) (goatools.goea.algorithms.GoeaAlgorithm method) (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll method) (goatools.parsers.ncbi_gene_file_reader.NCBIgeneFileReader method) run_study() (goatools.go_enrichment.GOEnrichmentStudy method) (goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS method) run_study_nts() (goatools.go_enrichment.GOEnrichmentStudy method) S schlicker_sim() (in module goatools.semantic) schlicker_sim_calc() (in module goatools.semantic) secdflt (goatools.grouper.hdrgos.HdrgosSections attribute) semantic_distance() (in module goatools.semantic) semantic_similarity() (in module goatools.semantic) set_corrected_pval() (goatools.go_enrichment.GOEnrichmentRecord method) set_correction() (goatools.multiple_testing.Bonferroni method) (goatools.multiple_testing.HolmBonferroni method) (goatools.multiple_testing.Sidak method) set_goid2color_pval() (goatools.gosubdag.plot.goea_results.GoeaResults method) set_goterm() (goatools.go_enrichment.GOEnrichmentRecord method) set_xlsx_colwidths() (goatools.wr_tbl_class.WrXlsx static method) shorten_go_name_all() (in module goatools.gosubdag.plot.go_name_shorten) shorten_go_name_ptbl1() (in module goatools.gosubdag.plot.go_name_shorten) shorten_go_name_ptbl3() (in module goatools.gosubdag.plot.go_name_shorten) shortest_path() (in module goatools.semantic) Sidak (class in goatools.multiple_testing) sort_nts() (goatools.evidence_codes.EvidenceCodes method) sortby() (goatools.grouper.sorter_gos.SorterGoIds method) Sorter (class in goatools.grouper.sorter) SorterGoIds (class in goatools.grouper.sorter_gos) SorterNts (class in goatools.grouper.sorter_nts) source (goatools.multiple_testing.Methods.NtMethodInfo attribute) spec_req1 (goatools.anno.init.reader_gaf.GafData attribute) species (goatools.anno.dnld_ebi_goa.DnldGoa attribute) species_items (goatools.anno.dnld_ebi_goa.DnldGoa attribute) srch_py_goids (goatools.grouper.read_goids.ReadGoids attribute) srch_py_section (goatools.grouper.read_goids.ReadGoids attribute) srch_section (goatools.grouper.read_goids.ReadGoids attribute) SsWang (class in goatools.semsim.termwise.wang) StatsDescribe (class in goatools.statsdescribe) str2ns (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr attribute) str_fmthdr() (goatools.gosubdag.plot.go_node.GoNode method) str_hdr() (goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll method) (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) str_rel_short() (goatools.godag.relationship_str.RelationshipStr method) str_relationships() (goatools.godag.relationship_str.RelationshipStr method) str_relationships_rev() (goatools.godag.relationship_str.RelationshipStr method) str_summaryline() (goatools.grouper.aart_geneproducts_one.AArtGeneProductSetsOne method) study_ids (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) study_n (goatools.goea.algorithms.base.GoeaContext attribute) (goatools.goea.algorithms.GoeaContext attribute) summarize_sec2hdrgos() (goatools.grouper.tasks.SummarySec2dHdrGos method) summarize_sec2hdrnts() (goatools.grouper.tasks.SummarySec2dHdrGos method) SummarySec2dHdrGos (class in goatools.grouper.tasks) T taxid_dflt (goatools.anno.init.reader_genetogo.InitAssc attribute) TermCounts (class in goatools.semantic) tic (goatools.anno.annoreader_base.AnnoReaderBase attribute) TopologicalSortRelationships (class in goatools.gosubdag.go_tasks) tsv_to_py() (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli method) tsv_to_py_all() (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli method) tsv_to_py_each() (goatools.cli.ncbi_gene_results_to_python.NCBIgeneToPythonCli method) TypeDef (class in goatools.godag.typedef) U ungzipper() (in module goatools.base) update_association() (goatools.anno.annoreader_base.AnnoReaderBase static method) (goatools.obo_parser.GODag method) (in module goatools.anno.update_association) update_rec() (goatools.godag.obo_optional_attributes.OboOptionalAttrs method) update_remaining_fldsdefprt() (goatools.go_enrichment.GOEnrichmentRecord method) V valid_formats (goatools.anno.annoreader_base.AnnoReaderBase attribute) validate() (goatools.anno.init.reader_gaf.GafHdr method) W WbFmt (class in goatools.wr_tbl_class) wr_data() (goatools.wr_tbl_class.WrXlsx method) wr_hdrs() (goatools.wr_tbl_class.WrXlsx method) wr_id2gos() (goatools.anno.idtogos_reader.IdToGosReader static method) wr_py_goea_results() (goatools.go_enrichment.GOEnrichmentStudy method) wr_py_nts() (in module goatools.nt_utils) wr_py_sections() (goatools.grouper.wr_sections.WrSectionsPy method) wr_py_sections_new() (goatools.grouper.wr_sections.WrSectionsPy method) wr_pydot_dag() (goatools.gosubdag.plot.gosubdag_plot.GoSubDagPlot method) wr_row_mergeall() (goatools.wr_tbl_class.WrXlsx method) wr_tex() (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr method) wr_title() (goatools.wr_tbl_class.WrXlsx method) wr_tsv() (goatools.cli.find_enrichment.GrpWr method) (goatools.go_enrichment.GOEnrichmentStudy method) (goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS method) (in module goatools.wr_tbl) wr_txt() (goatools.anno.gaf_reader.GafReader static method) (goatools.cli.find_enrichment.GrpWr method) (goatools.go_enrichment.GOEnrichmentStudy method) (goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS method) (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr method) (goatools.rpt.rpt_lev_depth.RptLevDepth method) wr_txt_gos() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) wr_txt_grouping_gos() (goatools.grouper.wr_sections.WrSectionsTxt method) wr_txt_nts() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) wr_txt_section_hdrgos() (goatools.grouper.wr_sections.WrSectionsTxt method) wr_xlsx() (goatools.cli.find_enrichment.GrpWr method) (goatools.go_enrichment.GOEnrichmentStudy method) (goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS method) (goatools.gosubdag.rpt.wr_xlsx.GoDepth1LettersWr method) (goatools.gosubdag.rpt.wr_xlsx.GoSubDagWr method) (goatools.parsers.david_chart.DavidChartReader method) (goatools.rpt.rpt_lev_depth.RptLevDepth method) (in module goatools.wr_tbl) wr_xlsx_gos() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) wr_xlsx_nts() (goatools.grouper.wrxlsx.WrXlsxSortedGos method) wr_xlsx_sections() (goatools.gosubdag.rpt.wr_xlsx.GoSubDagWr method) (in module goatools.wr_tbl) WrHierCli (class in goatools.cli.wr_hierarchy) WrHierGO (class in goatools.gosubdag.rpt.write_hierarchy) WrHierPrt (class in goatools.rpt.write_hierarchy_base) write() (goatools.cli.compare_gos.CompareGOsCli method) write_dag() (goatools.obo_parser.GODag method) write_summary_cnts() (goatools.rpt.rpt_lev_depth.RptLevDepth method) write_summary_cnts_all() (goatools.rpt.rpt_lev_depth.RptLevDepth method) write_summary_cnts_goobjs() (goatools.rpt.rpt_lev_depth.RptLevDepth method) wrplt() (goatools.grouper.plotobj.GoSubDagPlotNt method) WrSectionsBase (class in goatools.grouper.wr_sections) WrSectionsCli (class in goatools.cli.wr_sections) WrSectionsPy (class in goatools.grouper.wr_sections) WrSectionsTxt (class in goatools.grouper.wr_sections) wrtxt_hier() (goatools.cli.wr_hierarchy.WrHierCli method) WrXlsx (class in goatools.wr_tbl_class) WrXlsxParams (class in goatools.wr_tbl_class) WrXlsxSortedGos (class in goatools.grouper.wrxlsx)