tanghaibao/goatools issues and pull requests

#207 - Installation issue: Invalid syntax

Issue - State: closed - Opened by ThHarbig almost 4 years ago - 3 comments

#206 - Request: add methods to convert DAGs to networkx graphs

Issue - State: closed - Opened by AoifeHughes almost 4 years ago - 3 comments

#205 - GOEA as in the jupyter notebook with my own files

Issue - State: closed - Opened by ziphra almost 4 years ago - 2 comments

#204 - How can i get def in obo file?

Issue - State: closed - Opened by Lix1993 almost 4 years ago - 2 comments

#203 - Installation or PATH issue

Issue - State: closed - Opened by johnacurtin almost 4 years ago - 4 comments

#202 - Goatools not accepting Human Phenotype Ontology (HPO) obo file and annotation.

Issue - State: closed - Opened by ecgenomics almost 4 years ago - 8 comments

#201 - gaf2.2 format support

Issue - State: closed - Opened by klausqian almost 4 years ago - 2 comments

#200 - Support for Ensembl IDs

Issue - State: closed - Opened by detrout about 4 years ago - 2 comments

#199 - Add license scan report and status

Pull Request - State: closed - Opened by fossabot about 4 years ago

#198 - connection refused in download_ncbi_associations

Issue - State: closed - Opened by ernestmordret about 4 years ago - 1 comment

#197 - Conda recipe missing required library

Issue - State: closed - Opened by genignored about 4 years ago - 4 comments

#194 - Ancestors considering specific relations

Issue - State: closed - Opened by rashmie about 4 years ago - 8 comments

#189 - Test with Python 3.9

Pull Request - State: closed - Opened by tanghaibao about 4 years ago - 3 comments

#183 - Wangs semantic similarity method

Issue - State: closed - Opened by ThHarbig over 4 years ago - 22 comments

#176 - Where to find background_genes_ncbi notebook?

Issue - State: closed - Opened by mcsimenc over 4 years ago - 1 comment

#169 - uncorrected p-value methods give different results

Issue - State: closed - Opened by emilyyaklich over 4 years ago - 1 comment

#168 - conda install goatools fails on win64 with nvidia gpu

Issue - State: closed - Opened by simonwm over 4 years ago - 1 comment
Labels: help wanted

#166 - p-value calculation discrepancy

Issue - State: closed - Opened by jvivian-atreca over 4 years ago - 1 comment

#164 - Cannot read supplemental table 4

Issue - State: closed - Opened by IrinnaP over 4 years ago - 1 comment

#162 - Comparison of GO Terms between list

Issue - State: closed - Opened by BioinformaNicks almost 5 years ago - 7 comments
Labels: TODO

#161 - import from genes_NCBI_10090_ProteinCoding results in unresolved reference

Issue - State: closed - Opened by rewatitappu almost 5 years ago - 3 comments

#160 - mismatch between go.values and get_all_children

Issue - State: closed - Opened by mdanb almost 5 years ago - 1 comment

#159 - Use a logging module for global-controlled logging level

Issue - State: closed - Opened by dvklopfenstein almost 5 years ago - 1 comment
Labels: enhancement

#152 - map_to_slim.py error

Issue - State: closed - Opened by yuanning-li about 5 years ago - 3 comments

#149 - SystemExit (from goatools.anno.init.reader_gaf)

Issue - State: closed - Opened by cross12tamu about 5 years ago - 2 comments

#148 - Calculating Lin's Similarity if a gene in the pair is not annotated

Issue - State: closed - Opened by serbulent about 5 years ago - 7 comments
Labels: High Priority

#147 - NCBI annotations: Use get_ns2assc() to combined species annotations

Issue - State: closed - Opened by tanghaibao about 5 years ago - 4 comments
Labels: High Priority

#137 - Great idea - clunky API and uninformative usage examples

Issue - State: closed - Opened by ialbert over 5 years ago - 12 comments
Labels: backlog

#135 - keyerror when running run.sh

Issue - State: closed - Opened by HaoruiZhang over 5 years ago - 1 comment

#133 - Enhancement: Add kws for quiet printing throughout the library

Issue - State: closed - Opened by AoifeHughes over 5 years ago - 6 comments

#130 - Error: Only few genes/proteins in the study are found in the background population.

Issue - State: open - Opened by arumds over 5 years ago - 6 comments

#113 - Plot all the significant GOterms from custom association file

Issue - State: open - Opened by rafarios50 over 6 years ago - 1 comment

#106 - Different enrichment results between after issue #96 fix

Issue - State: closed - Opened by hag007 over 6 years ago - 6 comments

#102 - is it possible to plot a list of GO terms?

Issue - State: closed - Opened by ghost over 6 years ago - 10 comments

#100 - error when running python scripts/plot_go_term.py --term=GO:####### --gml

Issue - State: closed - Opened by r1-12king over 6 years ago - 2 comments

#99 - very large pvalue qvalue difference

Issue - State: open - Opened by linsson over 6 years ago - 8 comments

#97 - About the latest version (running error)

Issue - State: closed - Opened by GuilleChapin over 6 years ago - 5 comments

#94 - Add "force_dnld" parameter and other improvements to download functions in base.py/associations.py

Issue - State: closed - Opened by Melnorme1984 about 7 years ago - 2 comments
Labels: help wanted, enhancement

#87 - conda does not install properly when using python 3.4

Issue - State: closed - Opened by JudoWill over 7 years ago - 3 comments
Labels: help wanted

#71 - Consider support for obographs json format

Issue - State: open - Opened by cmungall over 8 years ago - 6 comments
Labels: TODO

#46 - Comparison studies and fisher.pvalue_population

Issue - State: closed - Opened by yunesj about 9 years ago - 1 comment

#45 - Loci with no GO annotation

Issue - State: closed - Opened by AGrusz about 9 years ago - 1 comment

GitHub / tanghaibao/goatools issues and pull requests