tanghaibao/goatools issues and pull requests

#308 - update init.py

Pull Request - State: closed - Opened by tanghaibao 3 months ago

#307 - Where to store obo file

Issue - State: closed - Opened by Tim-Kirkwood 3 months ago - 1 comment

#306 - No TAXID for Ecoli and incompatibility of the Ecoli specific annotation file

Issue - State: open - Opened by FH96 3 months ago

#305 - Extra 'label' node at top of DAG of GO terms

Issue - State: open - Opened by avigailtaylor 4 months ago

#304 - I couldn't get "regulates" ancestors terms

Issue - State: open - Opened by 10myl200 5 months ago - 7 comments
Labels: bug

#303 - Fix obsolete unicode functions from py2 (thanks @aipolly, #266)

Pull Request - State: closed - Opened by tanghaibao 7 months ago

#302 - Dev

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#301 - change back to macos-latest

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#300 - Update README

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#299 - Fix setup.cfg to include setuptools

Pull Request - State: closed - Opened by iosonofabio 8 months ago - 1 comment

#298 - setuptools required

Issue - State: closed - Opened by iosonofabio 8 months ago - 4 comments

#297 - Replace super(Class, self) => super()

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#296 - Add encoding="utf-8" in find_enrichment.py

Pull Request - State: closed - Opened by tanghaibao 8 months ago

#295 - Error: Unicode Decode Error

Issue - State: closed - Opened by yb520abab 9 months ago - 2 comments

#294 - Fix FTP calls and remove loading_bar

Pull Request - State: closed - Opened by tanghaibao 9 months ago

#293 - Add test_godag_ecs() per #292

Pull Request - State: closed - Opened by tanghaibao 9 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 9 months ago - 1 comment

#291 - Keeping terms not in DAG

Issue - State: open - Opened by Prunoideae 9 months ago - 2 comments

#290 - Question about map_to_slim

Issue - State: closed - Opened by juanjo255 9 months ago

#289 - implement graph orientation change (graphviz rankdir)

Pull Request - State: closed - Opened by SchwarzMarek 10 months ago

#288 - Left to right plot in go_plot.py?

Issue - State: closed - Opened by SchwarzMarek 11 months ago - 1 comment

#287 - goatools v1.3.11 seems cannot handle the header of GAF2.2

Issue - State: closed - Opened by jiaow1018 11 months ago

#286 - Text in GO term box - plotting

Issue - State: open - Opened by LeilaFattel 12 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 about 1 year ago - 2 comments

#284 - Added Schlicker's Similarity Measure

Pull Request - State: closed - Opened by Piquipato about 1 year ago - 1 comment

#283 - Add test_multiple_testing

Pull Request - State: closed - Opened by tanghaibao about 1 year ago

#282 - bug fix/enhancement HolmBonferroni correction

Pull Request - State: closed - Opened by RossLabCSU about 1 year ago

#281 - HolmBonferroni correction generates error with certain p-value lists

Issue - State: closed - Opened by RossLabCSU over 1 year ago - 3 comments
Labels: enhancement, bug

#280 - Remove extra comma in goea_nbt3102.ipyb (thanks @Pooryamb, #279)

Pull Request - State: closed - Opened by tanghaibao over 1 year ago

#279 - Issue with goea_nbt3102.ipynb

Issue - State: closed - Opened by Pooryamb over 1 year ago - 1 comment

#278 - Initial implementation of a central logger (#159)

Pull Request - State: closed - Opened by tanghaibao over 1 year ago

#277 - Better support for obsolete terms (#276, thanks @Maxim-Karpov)

Pull Request - State: closed - Opened by tanghaibao over 1 year ago

#276 - Potential bug: "WARNING: GO:0006379 NOT FOUND IN DAG"

Issue - State: closed - Opened by Maxim-Karpov over 1 year ago - 7 comments

#275 - AttributeError In godag/gp_taks.py file

Issue - State: closed - Opened by dinavod12 over 1 year ago - 3 comments

#274 - Error in making result file

Issue - State: closed - Opened by Rhia15 over 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 over 1 year ago - 1 comment

#272 - Optimising go term tests

Issue - State: open - Opened by francicco over 1 year ago

#271 - What's the point of removing genes with identical identifiers?

Issue - State: open - Opened by shelkmike over 1 year ago

#270 - Information content of a custom GO annotation.

Issue - State: open - Opened by ohdongha almost 2 years ago - 1 comment

#269 - regarding obsolete terms

Issue - State: closed - Opened by Danablesson almost 2 years ago

#268 - Update workflow version

Pull Request - State: closed - Opened by tanghaibao almost 2 years ago

#267 - Best practices for background gene sets

Issue - State: closed - Opened by stanleyjs almost 2 years ago - 3 comments

#266 - function unicode and unichr depreciated in python3

Issue - State: closed - Opened by aipolly almost 2 years ago

#265 - update goea_nbt3102 notebook

Pull Request - State: closed - Opened by siebrenf almost 2 years ago

#264 - Conditional tests?

Issue - State: open - Opened by sjfleming almost 2 years ago
Labels: enhancement

#263 - Idea: Flag to compute enrichment for user-specified GO terms

Issue - State: open - Opened by DylanSteinecke almost 2 years ago
Labels: enhancement

#262 - p_value calculation with fisher_exact

Issue - State: closed - Opened by Maryam-Haghani almost 2 years ago - 2 comments

#261 - p-value calculation with fisher

Issue - State: closed - Opened by Maryam-Haghani almost 2 years ago

#260 - Keep on receiving **FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS in my current work

Issue - State: open - Opened by HelloWorldLTY almost 2 years 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 about 2 years ago - 1 comment

#258 - Try remove xlrd version

Pull Request - State: closed - Opened by tanghaibao about 2 years ago - 1 comment

#257 - (Made a mistake)

Issue - State: closed - Opened by jasperhyp about 2 years ago

#256 - How to get most recent common ancesters and shortest path distance between two terms?

Issue - State: open - Opened by jasperhyp about 2 years ago

#255 - Update ECO codes

Pull Request - State: closed - Opened by dvklopfenstein about 2 years ago

#254 - Error: no population items seen in the annotations when using GAF file

Issue - State: open - Opened by jlastoll about 2 years ago - 1 comment

#253 - Added GPAD annotation notebook

Pull Request - State: closed - Opened by dvklopfenstein about 2 years ago

#252 - Migrate the build system to pyproject.toml

Pull Request - State: closed - Opened by tanghaibao about 2 years ago

#251 - An example of GOEA with Uniprots

Issue - State: closed - Opened by Maryam-Haghani about 2 years ago - 6 comments

#250 - Output columns of grouped_gos

Issue - State: open - Opened by cestaroa about 2 years ago

#249 - Some questions about gene selection

Issue - State: open - Opened by HelloWorldLTY over 2 years ago

#248 - AttributeError: 'GOEnrichmentStudy' object has no attribute 'print_results'

Issue - State: open - Opened by Liyong-Zhang over 2 years ago

#247 - Error message while running goatools

Issue - State: open - Opened by akaur1988 over 2 years ago

#246 - NOT FOUND IN DAG

Issue - State: closed - Opened by msheltra over 2 years ago - 3 comments

#244 - Does gene ontology enrichment analysis work with Ensembl gene ids?

Issue - State: open - Opened by BerkKilicoglu over 2 years ago

#243 - Discrepancies between using GoSearch and direct search on geneontology.org

Issue - State: open - Opened by jasperhyp over 2 years ago - 1 comment

#242 - Issue with `plot_gos()`

Issue - State: closed - Opened by stefan-dam over 2 years ago - 1 comment

#241 - Unhelpful Documentation, Missing High Level Interface

Issue - State: open - Opened by fratajcz over 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 almost 3 years ago

#239 - Check `log` before print() in go_enrichment.py (thanks @illumination-k, #238)

Pull Request - State: closed - Opened by tanghaibao almost 3 years ago

#238 - `log = None` cannot complete suppress stdout in GOEnrichmentStudyNS

Issue - State: closed - Opened by illumination-k almost 3 years ago - 2 comments

#237 - Handle EC.5.3.3.21

Pull Request - State: closed - Opened by tanghaibao almost 3 years ago

#236 - Small changes according to issue 235

Pull Request - State: closed - Opened by yotamcons almost 3 years ago

#235 - a couple of small issues with the readme

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

#234 - Updated code for PR232 (wget no longer required)

Pull Request - State: closed - Opened by dvklopfenstein about 3 years ago

#233 - Allow parsing of "xref: EC x.x.x.x"

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

#232 - Remove false requirement

Pull Request - State: closed - Opened by flying-sheep about 3 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 about 3 years ago

#230 - download_ncbi_associations() fails while decompressing file

Issue - State: closed - Opened by msbentsen over 3 years ago - 2 comments

#229 - Allow arbitrary Aspect codes

Pull Request - State: closed - Opened by serenalotreck over 3 years ago

#228 - Allow arbitrary letters in Aspect column

Issue - State: closed - Opened by serenalotreck over 3 years ago - 2 comments

#227 - Rename backround_genes_ncbi.ipynb to background_genes_ncbi.ipynb

Pull Request - State: closed - Opened by abearab over 3 years ago

#226 - Incorrect data file for notebook : Run a Gene Ontology Enrichment Analysis (GOEA)

Issue - State: closed - Opened by vwongjun over 3 years ago - 2 comments

#225 - render DAG w JSON

Issue - State: open - Opened by chrispam10 over 3 years ago - 2 comments

#224 - Issues Generating Background GeneSet

Issue - State: open - Opened by TTCooper-PhD over 3 years ago - 1 comment

#223 - questions about semantic similarity notebook

Issue - State: open - Opened by sunyi000 over 3 years ago

#222 - Update wget go-basic.obo

Pull Request - State: closed - Opened by tanghaibao over 3 years ago - 1 comment

#221 - Added option no_dup to WrHierGO.

Pull Request - State: closed - Opened by avigailtaylor over 3 years ago - 1 comment

#220 - I got confusing results during GOEA

Issue - State: closed - Opened by WinterFor over 3 years ago - 5 comments

#219 - Fixed bug in write_hierarchy_base.py

Pull Request - State: closed - Opened by avigailtaylor over 3 years ago - 3 comments

#218 - AssertionError: **FATAL: NO TAXIDS: gene2go, When I use `taxids = [9541]`

Issue - State: closed - Opened by WinterFor over 3 years ago - 6 comments

#217 - Fold change or any kind of the enrichment score

Issue - State: open - Opened by hsiaoyi0504 over 3 years ago

#216 - Remove p-value calc using fisher package (thanks @emilyyaklich, #169)

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

#215 - Support geneIDs passed in as numpy array (thanks @wu-diana, #214)

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

#214 - study (geneIDs) cannot be a numpy array

Issue - State: closed - Opened by wu-diana over 3 years ago - 1 comment

#213 - basic validity checks of id2gos association file

Issue - State: open - Opened by orenmn over 3 years ago - 2 comments
Labels: help wanted

#212 - Question: DAGs like how AgriGO or topGO do

Issue - State: open - Opened by harish0201 over 3 years ago - 2 comments

#211 - Add analysis of term counting (thanks @mdanb, #160)

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

#210 - Improve documentation for release v1.1.5

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

#209 - Don't display ERROR in get_id2gos (thanks @yuanning-li, #152)

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

#208 - Add support for GAF2.2 (thanks @klausqian, #201)

Pull Request - State: closed - Opened by tanghaibao over 3 years ago

GitHub / tanghaibao/goatools issues and pull requests