tanghaibao goatools issues

tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms

BSD 2-Clause "Simplified" License

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Try remove xlrd version

#258 tanghaibao closed 1 year ago
1
(Made a mistake)

#257 jasperhyp closed 1 year ago
0
How to get most recent common ancesters and shortest path distance between two terms?

#256 jasperhyp opened 1 year ago
0
Update ECO codes

#255 dvklopfenstein closed 1 year ago
0
Error: no population items seen in the annotations when using GAF file

#254 jlastoll opened 1 year ago
1
Added GPAD annotation notebook

#253 dvklopfenstein closed 2 years ago
0
Migrate the build system to pyproject.toml

#252 tanghaibao closed 2 years ago
0
An example of GOEA with Uniprots

#251 Maryam-Haghani closed 5 months ago
6
Output columns of grouped_gos

#250 cestaroa opened 2 years ago
0
Some questions about gene selection

#249 HelloWorldLTY opened 2 years ago
0
AttributeError: 'GOEnrichmentStudy' object has no attribute 'print_results'

#248 Liyong-Zhang opened 2 years ago
0
Error message while running goatools

#247 akaur1988 opened 2 years ago
0
NOT FOUND IN DAG

#246 msheltra closed 2 years ago
3
Does gene ontology enrichment analysis work with Ensembl gene ids?

#244 BerkKilicoglu opened 2 years ago
0
Discrepancies between using GoSearch and direct search on geneontology.org

#243 jasperhyp opened 2 years ago
1
Issue with `plot_gos()`

#242 stefan-dam closed 1 year ago
1
Unhelpful Documentation, Missing High Level Interface

#241 fratajcz opened 2 years ago
5
cannot import name 'ncbi_tsv_to_py' from 'goatools.cli.ncbi_gene_results_to_python'

#240 jjacobsli opened 2 years ago
0
Check `log` before print() in go_enrichment.py (thanks @illumination-k, #238)

#239 tanghaibao closed 2 years ago
0
`log = None` cannot complete suppress stdout in GOEnrichmentStudyNS

#238 illumination-k closed 2 years ago
2
Handle EC.5.3.3.21

#237 tanghaibao closed 2 years ago
0
Small changes according to issue 235

#236 yotamcons closed 2 years ago
0
a couple of small issues with the readme

#235 yotamcons closed 2 years ago
5
Updated code for PR232 (wget no longer required)

#234 dvklopfenstein closed 2 years ago
0
Allow parsing of "xref: EC x.x.x.x"

#233 tanghaibao closed 2 years ago
0
Remove false requirement

#232 flying-sheep closed 2 years ago
3
Added function to convert one NCBI Gene tsv file to a Python module.

#231 dvklopfenstein closed 3 years ago
0
download_ncbi_associations() fails while decompressing file

#230 msbentsen closed 3 years ago
2
Allow arbitrary Aspect codes

#229 serenalotreck closed 3 years ago
0
Allow arbitrary letters in Aspect column

#228 serenalotreck closed 3 years ago
2
Rename backround_genes_ncbi.ipynb to background_genes_ncbi.ipynb

#227 abearab closed 3 years ago
0
Incorrect data file for notebook : Run a Gene Ontology Enrichment Analysis (GOEA)

#226 vwongjun closed 3 years ago
2
render DAG w JSON

#225 chrispam10 opened 3 years ago
2
Issues Generating Background GeneSet

#224 TTCooper-PhD opened 3 years ago
1
questions about semantic similarity notebook

#223 sunyi000 opened 3 years ago
0
Update wget go-basic.obo

#222 tanghaibao closed 3 years ago
1
Added option no_dup to WrHierGO.

#221 avigailtaylor closed 3 years ago
1
I got confusing results during GOEA

#220 WinterFor opened 3 years ago
5
Fixed bug in write_hierarchy_base.py

#219 avigailtaylor closed 3 years ago
3
AssertionError: **FATAL: NO TAXIDS: gene2go, When I use `taxids = [9541]`

#218 WinterFor closed 3 years ago
6
Fold change or any kind of the enrichment score

#217 hsiaoyi0504 opened 3 years ago
0
Remove p-value calc using fisher package (thanks @emilyyaklich, #169)

#216 tanghaibao closed 3 years ago
0
Support geneIDs passed in as numpy array (thanks @wu-diana, #214)

#215 tanghaibao closed 3 years ago
0
study (geneIDs) cannot be a numpy array

#214 wu-diana closed 2 years ago
1
basic validity checks of id2gos association file

#213 orenmn opened 3 years ago
2
Question: DAGs like how AgriGO or topGO do

#212 harish0201 opened 3 years ago
2
Add analysis of term counting (thanks @mdanb, #160)

#211 tanghaibao closed 3 years ago
0
Improve documentation for release v1.1.5

#210 tanghaibao closed 3 years ago
0
Don't display ERROR in get_id2gos (thanks @yuanning-li, #152)

#209 tanghaibao closed 3 years ago
0
Add support for GAF2.2 (thanks @klausqian, #201)

#208 tanghaibao closed 3 years ago
0

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