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

#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

#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

#286 - Text in GO term box - plotting

Issue - State: open - Opened by LeilaFattel 5 months ago

#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

#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

#272 - Optimising go term tests

Issue - State: open - Opened by francicco 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

#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

#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

#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

#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

#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

#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

#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