Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / tanghaibao/goatools issues and pull requests
#303 - Fix obsolete unicode functions from py2 (thanks @aipolly, #266)
Pull Request -
State: closed - Opened by tanghaibao 3 days ago
#302 - Dev
Pull Request -
State: closed - Opened by tanghaibao 14 days ago
#301 - change back to macos-latest
Pull Request -
State: closed - Opened by tanghaibao 19 days ago
#300 - Update README
Pull Request -
State: closed - Opened by tanghaibao 19 days ago
#299 - Fix setup.cfg to include setuptools
Pull Request -
State: closed - Opened by iosonofabio 27 days ago
- 1 comment
#298 - setuptools required
Issue -
State: closed - Opened by iosonofabio 27 days ago
- 4 comments
#297 - Replace super(Class, self) => super()
Pull Request -
State: closed - Opened by tanghaibao 30 days ago
#296 - Add encoding="utf-8" in find_enrichment.py
Pull Request -
State: closed - Opened by tanghaibao about 1 month ago
#295 - Error: Unicode Decode Error
Issue -
State: closed - Opened by yb520abab about 1 month ago
- 2 comments
#294 - Fix FTP calls and remove loading_bar
Pull Request -
State: closed - Opened by tanghaibao about 2 months ago
#293 - Add test_godag_ecs() per #292
Pull Request -
State: closed - Opened by tanghaibao about 2 months ago
#292 - [Question] How to parse .json, .obo, or .owl to get dictionary of enzymes {id_go:{ec_1, ec_2, ..., ec_n}}
Issue -
State: closed - Opened by jolespin 2 months ago
- 1 comment
#291 - Keeping terms not in DAG
Issue -
State: open - Opened by Prunoideae 2 months ago
- 2 comments
#290 - Question about map_to_slim
Issue -
State: open - Opened by juanjo255 2 months ago
#289 - implement graph orientation change (graphviz rankdir)
Pull Request -
State: closed - Opened by SchwarzMarek 3 months ago
#288 - Left to right plot in go_plot.py?
Issue -
State: closed - Opened by SchwarzMarek 4 months ago
- 1 comment
#287 - goatools v1.3.11 seems cannot handle the header of GAF2.2
Issue -
State: closed - Opened by jiaow1018 4 months ago
#286 - Text in GO term box - plotting
Issue -
State: open - Opened by LeilaFattel 5 months ago
#285 - Do anyone know the differences between the enriched results and the purifed results after the GOEA analysis of the GOATOOLS?
Issue -
State: closed - Opened by Sotdo 7 months ago
- 2 comments
#284 - Added Schlicker's Similarity Measure
Pull Request -
State: closed - Opened by Piquipato 7 months ago
- 1 comment
#283 - Add test_multiple_testing
Pull Request -
State: closed - Opened by tanghaibao 8 months ago
#282 - bug fix/enhancement HolmBonferroni correction
Pull Request -
State: closed - Opened by RossLabCSU 8 months ago
#281 - HolmBonferroni correction generates error with certain p-value lists
Issue -
State: closed - Opened by RossLabCSU 8 months ago
- 3 comments
Labels: enhancement, bug
#280 - Remove extra comma in goea_nbt3102.ipyb (thanks @Pooryamb, #279)
Pull Request -
State: closed - Opened by tanghaibao 9 months ago
#279 - Issue with goea_nbt3102.ipynb
Issue -
State: closed - Opened by Pooryamb 9 months ago
- 1 comment
#278 - Initial implementation of a central logger (#159)
Pull Request -
State: closed - Opened by tanghaibao 9 months ago
#277 - Better support for obsolete terms (#276, thanks @Maxim-Karpov)
Pull Request -
State: closed - Opened by tanghaibao 9 months ago
#276 - Potential bug: "WARNING: GO:0006379 NOT FOUND IN DAG"
Issue -
State: closed - Opened by Maxim-Karpov 9 months ago
- 7 comments
#275 - AttributeError In godag/gp_taks.py file
Issue -
State: closed - Opened by dinavod12 10 months ago
- 3 comments
#274 - Error in making result file
Issue -
State: open - Opened by Rhia15 about 1 year ago
- 3 comments
#273 - Issues with find.enrichment.py when I use the same IDs for study.txt and population.txt
Issue -
State: open - Opened by pomorale about 1 year ago
- 1 comment
#272 - Optimising go term tests
Issue -
State: open - Opened by francicco about 1 year ago
#271 - What's the point of removing genes with identical identifiers?
Issue -
State: open - Opened by shelkmike about 1 year ago
#270 - Information content of a custom GO annotation.
Issue -
State: open - Opened by ohdongha about 1 year ago
- 1 comment
#269 - regarding obsolete terms
Issue -
State: closed - Opened by Danablesson about 1 year ago
#268 - Update workflow version
Pull Request -
State: closed - Opened by tanghaibao about 1 year ago
#267 - Best practices for background gene sets
Issue -
State: open - Opened by stanleyjs over 1 year ago
- 3 comments
#266 - function unicode and unichr depreciated in python3
Issue -
State: closed - Opened by aipolly over 1 year ago
#265 - update goea_nbt3102 notebook
Pull Request -
State: closed - Opened by siebrenf over 1 year ago
#264 - Conditional tests?
Issue -
State: open - Opened by sjfleming over 1 year ago
Labels: enhancement
#263 - Idea: Flag to compute enrichment for user-specified GO terms
Issue -
State: open - Opened by DylanSteinecke over 1 year ago
Labels: enhancement
#262 - p_value calculation with fisher_exact
Issue -
State: closed - Opened by Maryam-Haghani over 1 year ago
- 2 comments
#261 - p-value calculation with fisher
Issue -
State: closed - Opened by Maryam-Haghani over 1 year ago
#260 - Keep on receiving **FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS in my current work
Issue -
State: open - Opened by HelloWorldLTY over 1 year ago
#259 - Different results when restricting background set to only include genes with at least one annotation term
Issue -
State: open - Opened by Maryam-Haghani over 1 year ago
- 1 comment
#258 - Try remove xlrd version
Pull Request -
State: closed - Opened by tanghaibao over 1 year ago
- 1 comment
#257 - (Made a mistake)
Issue -
State: closed - Opened by jasperhyp over 1 year ago
#256 - How to get most recent common ancesters and shortest path distance between two terms?
Issue -
State: open - Opened by jasperhyp over 1 year ago
#255 - Update ECO codes
Pull Request -
State: closed - Opened by dvklopfenstein over 1 year ago
#254 - Error: no population items seen in the annotations when using GAF file
Issue -
State: open - Opened by jlastoll over 1 year ago
- 1 comment
#253 - Added GPAD annotation notebook
Pull Request -
State: closed - Opened by dvklopfenstein over 1 year ago
#252 - Migrate the build system to pyproject.toml
Pull Request -
State: closed - Opened by tanghaibao over 1 year ago
#251 - An example of GOEA with Uniprots
Issue -
State: open - Opened by Maryam-Haghani over 1 year ago
- 6 comments
#250 - Output columns of grouped_gos
Issue -
State: open - Opened by cestaroa over 1 year ago
#249 - Some questions about gene selection
Issue -
State: open - Opened by HelloWorldLTY over 1 year ago
#248 - AttributeError: 'GOEnrichmentStudy' object has no attribute 'print_results'
Issue -
State: open - Opened by Liyong-Zhang almost 2 years ago
#247 - Error message while running goatools
Issue -
State: open - Opened by akaur1988 almost 2 years ago
#246 - NOT FOUND IN DAG
Issue -
State: closed - Opened by msheltra almost 2 years ago
- 3 comments
#244 - Does gene ontology enrichment analysis work with Ensembl gene ids?
Issue -
State: open - Opened by BerkKilicoglu almost 2 years ago
#243 - Discrepancies between using GoSearch and direct search on geneontology.org
Issue -
State: open - Opened by jasperhyp almost 2 years ago
- 1 comment
#242 - Issue with `plot_gos()`
Issue -
State: closed - Opened by stefan-dam about 2 years ago
- 1 comment
#241 - Unhelpful Documentation, Missing High Level Interface
Issue -
State: open - Opened by fratajcz about 2 years ago
- 5 comments
#240 - cannot import name 'ncbi_tsv_to_py' from 'goatools.cli.ncbi_gene_results_to_python'
Issue -
State: open - Opened by jjacobsli about 2 years ago
#239 - Check `log` before print() in go_enrichment.py (thanks @illumination-k, #238)
Pull Request -
State: closed - Opened by tanghaibao about 2 years ago
#238 - `log = None` cannot complete suppress stdout in GOEnrichmentStudyNS
Issue -
State: closed - Opened by illumination-k about 2 years ago
- 2 comments
#237 - Handle EC.5.3.3.21
Pull Request -
State: closed - Opened by tanghaibao over 2 years ago
#236 - Small changes according to issue 235
Pull Request -
State: closed - Opened by yotamcons over 2 years ago
#235 - a couple of small issues with the readme
Issue -
State: closed - Opened by yotamcons over 2 years ago
- 5 comments
#234 - Updated code for PR232 (wget no longer required)
Pull Request -
State: closed - Opened by dvklopfenstein over 2 years ago
#233 - Allow parsing of "xref: EC x.x.x.x"
Pull Request -
State: closed - Opened by tanghaibao over 2 years ago
#232 - Remove false requirement
Pull Request -
State: closed - Opened by flying-sheep over 2 years ago
- 3 comments
#231 - Added function to convert one NCBI Gene tsv file to a Python module.
Pull Request -
State: closed - Opened by dvklopfenstein over 2 years ago
#230 - download_ncbi_associations() fails while decompressing file
Issue -
State: closed - Opened by msbentsen over 2 years ago
- 2 comments
#229 - Allow arbitrary Aspect codes
Pull Request -
State: closed - Opened by serenalotreck over 2 years ago
#228 - Allow arbitrary letters in Aspect column
Issue -
State: closed - Opened by serenalotreck over 2 years ago
- 2 comments
#227 - Rename backround_genes_ncbi.ipynb to background_genes_ncbi.ipynb
Pull Request -
State: closed - Opened by abearab over 2 years ago
#226 - Incorrect data file for notebook : Run a Gene Ontology Enrichment Analysis (GOEA)
Issue -
State: closed - Opened by vwongjun over 2 years ago
- 2 comments
#225 - render DAG w JSON
Issue -
State: open - Opened by chrispam10 almost 3 years ago
- 2 comments
#224 - Issues Generating Background GeneSet
Issue -
State: open - Opened by TTCooper-PhD almost 3 years ago
- 1 comment
#223 - questions about semantic similarity notebook
Issue -
State: open - Opened by sunyi000 almost 3 years ago
#222 - Update wget go-basic.obo
Pull Request -
State: closed - Opened by tanghaibao almost 3 years ago
- 1 comment
#221 - Added option no_dup to WrHierGO.
Pull Request -
State: closed - Opened by avigailtaylor almost 3 years ago
- 1 comment
#220 - I got confusing results during GOEA
Issue -
State: open - Opened by WinterFor about 3 years ago
- 5 comments
#219 - Fixed bug in write_hierarchy_base.py
Pull Request -
State: closed - Opened by avigailtaylor about 3 years ago
- 3 comments
#218 - AssertionError: **FATAL: NO TAXIDS: gene2go, When I use `taxids = [9541]`
Issue -
State: closed - Opened by WinterFor about 3 years ago
- 6 comments
#217 - Fold change or any kind of the enrichment score
Issue -
State: open - Opened by hsiaoyi0504 about 3 years ago
#216 - Remove p-value calc using fisher package (thanks @emilyyaklich, #169)
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#215 - Support geneIDs passed in as numpy array (thanks @wu-diana, #214)
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#214 - study (geneIDs) cannot be a numpy array
Issue -
State: closed - Opened by wu-diana about 3 years ago
- 1 comment
#213 - basic validity checks of id2gos association file
Issue -
State: open - Opened by orenmn about 3 years ago
- 2 comments
Labels: help wanted
#212 - Question: DAGs like how AgriGO or topGO do
Issue -
State: open - Opened by harish0201 about 3 years ago
- 2 comments
#211 - Add analysis of term counting (thanks @mdanb, #160)
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#210 - Improve documentation for release v1.1.5
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#209 - Don't display ERROR in get_id2gos (thanks @yuanning-li, #152)
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#208 - Add support for GAF2.2 (thanks @klausqian, #201)
Pull Request -
State: closed - Opened by tanghaibao about 3 years ago
#207 - Installation issue: Invalid syntax
Issue -
State: closed - Opened by ThHarbig about 3 years ago
- 3 comments
#206 - Request: add methods to convert DAGs to networkx graphs
Issue -
State: open - Opened by AoifeHughes about 3 years ago
- 3 comments
#205 - GOEA as in the jupyter notebook with my own files
Issue -
State: closed - Opened by ziphra about 3 years ago
- 2 comments
#204 - How can i get def in obo file?
Issue -
State: closed - Opened by Lix1993 over 3 years ago
- 2 comments
#203 - Installation or PATH issue
Issue -
State: closed - Opened by johnacurtin over 3 years ago
- 4 comments