tanghaibao goatools issues

tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms

BSD 2-Clause "Simplified" License

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issues

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Installation or PATH issue

#203 johnacurtin closed 3 years ago
4
Goatools not accepting Human Phenotype Ontology (HPO) obo file and annotation.

#202 ecgenomics closed 2 years ago
8
gaf2.2 format support

#201 jwqian99 closed 3 years ago
2
Support for Ensembl IDs

#200 detrout closed 3 years ago
2
Add license scan report and status

#199 fossabot closed 3 years ago
0
connection refused in download_ncbi_associations

#198 ernestmordret closed 10 months ago
1
Conda recipe missing required library

#197 genignored opened 3 years ago
4
Getting information content (IC) using Pfam2GO

#196 dvklopfenstein closed 3 years ago
2
Error loading gaf file

#195 JanZrimec closed 3 years ago
4
Ancestors considering specific relations

#194 rashmie closed 1 month ago
8
Also remove `nose` from requirements.txt

#193 tanghaibao closed 3 years ago
0
Add tests_require (thanks @flying-sheep, #174)

#192 tanghaibao closed 3 years ago
0
Fix svg output dpi bug (thanks @illumination-k, #179)

#191 tanghaibao closed 3 years ago
0
Add test to ensure PACKAGES in setup.py show all subdirs in goatools dirs

#190 dvklopfenstein closed 3 years ago
1
Test with Python 3.9

#189 tanghaibao closed 3 years ago
3
Move reldepth calculations to its own module

#188 dvklopfenstein closed 3 years ago
2
compare_gos.py namedtuple error

#187 marade closed 3 years ago
10
How do I go from a list of genes to a list of intersecting pathways

#186 catskillsresearch opened 3 years ago
2
Update obo_parser.py

#185 Lix1993 closed 4 years ago
1
Not able to access all the paths from a term to the root

#184 DhananjayKimothi opened 4 years ago
1
Wangs semantic similarity method

#183 ThHarbig closed 3 years ago
22
fix gml export

#182 Lix1993 closed 4 years ago
1
cannot export gml file

#181 Lix1993 closed 4 years ago
1
Can i use goatools to get a go2ids file from id2gos

#180 Lix1993 closed 4 years ago
1
plot_go_term is not work well if format is svg

#179 illumination-k closed 3 years ago
0
What does R represent

#178 chestnzu1 closed 4 years ago
2
maximum recursion depth exceeded while calling a Python object

#177 z2e2 closed 3 years ago
2
Where to find background_genes_ncbi notebook?

#176 mcsimenc closed 3 years ago
1
how to find association_file?

#175 shiyi-pan closed 3 years ago
2
Remove test dependencies from requirements

#174 flying-sheep closed 3 years ago
0
Pronunciation (not a REAL issue)

#173 cross12tamu closed 4 years ago
2
GoaTools error ? (python plot_go_term.py --term=GO:0005737 --gml )

#172 sunnyEV closed 3 years ago
1
Recreate Table 2 showing descendant counts for depth-01 GO terms are highly skewed

#171 dvklopfenstein closed 4 years ago
1
Example error

#170 chestnzu1 closed 4 years ago
4
uncorrected p-value methods give different results

#169 emilyyaklich closed 3 years ago
1
conda install goatools fails on win64 with nvidia gpu

#168 simonwm closed 1 year ago
1
Error when importing wr_xlsx_gos

#167 tanghaibao closed 3 years ago
1
p-value calculation discrepancy

#166 jvivian-atreca closed 3 years ago
1
**FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS

#165 HLAvieira closed 4 years ago
7
Cannot read supplemental table 4

#164 IrinnaP closed 3 years ago
1
wr_hier.py only return GOterms in namespace 'BP'

#163 NewTearingHeaven closed 4 years ago
5
Comparison of GO Terms between list

#162 BioinformaNicks closed 3 years ago
7
import from genes_NCBI_10090_ProteinCoding results in unresolved reference

#161 rewatitappu closed 3 years ago
3
mismatch between go.values and get_all_children

#160 mdanb closed 3 years ago
1
Use a logging module for global-controlled logging level

#159 dvklopfenstein closed 3 months ago
1
Help to properly use the three files (study.txt, population.txt and associations.txt)

#158 gosalone closed 4 years ago
0
AttributeError: 'module' object has no attribute '__version__'

#157 gosalone closed 4 years ago
4
Information Content varies with version

#156 huhrichard closed 4 years ago
2
Remove GODag command output

#155 AgustinPardo closed 4 years ago
2
Retrieve "consider" key of the obsolete GO terms AttributeERROR

#154 AgustinPardo closed 4 years ago
4

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