tanghaibao/goatools

Issues

• Where to store obo file

  #307 opened 2 months ago by Tim-Kirkwood
  1

• No TAXID for Ecoli and incompatibility of the Ecoli specific annotation file

  #306 opened 2 months ago by FH96
  0

• Extra 'label' node at top of DAG of GO terms

  #305 opened 3 months ago by avigailtaylor
  0

• I couldn't get "regulates" ancestors terms

  #304 opened 3 months ago by 10myl200
  7

• Question about map_to_slim

  #290 opened 5 months ago by juanjo255
  0

• An example of GOEA with Uniprots

  #251 opened 6 months ago by Maryam-Haghani
  6

• function unicode and unichr depreciated in python3

  #266 opened 6 months ago by aipolly
  0

• Potential bug: "WARNING: GO:0006379 NOT FOUND IN DAG"

  #276 opened a year ago by Maxim-Karpov
  7

• setuptools required

  #298 opened 7 months ago by iosonofabio
  4

• Error: Unicode Decode Error

  #295 opened 7 months ago by yb520abab
  2

• [Question] How to parse .json, .obo, or .owl to get dictionary of enzymes {id_go:{ec_1, ec_2, ..., ec_n}}

  #292 opened 8 months ago by jolespin
  1

• Keeping terms not in DAG

  #291 opened 8 months ago by Prunoideae
  2

• Left to right plot in go_plot.py?

  #288 opened 8 months ago by SchwarzMarek
  1

• goatools v1.3.11 seems cannot handle the header of GAF2.2

  #287 opened 9 months ago by jiaow1018
  0

• Text in GO term box - plotting

  #286 opened a year ago by LeilaFattel
  0

• Do anyone know the differences between the enriched results and the purifed results after the GOEA analysis of the GOATOOLS?

  #285 opened a year ago by Sotdo
  2

• regarding obsolete terms

  #269 opened a year ago by Danablesson
  0

• AttributeError In godag/gp_taks.py file

  #275 opened a year ago by dinavod12
  3

• Issue with goea_nbt3102.ipynb

  #279 opened a year ago by Pooryamb
  1

• HolmBonferroni correction generates error with certain p-value lists

  #281 opened a year ago by RossLabCSU
  3

• Issue with `plot_gos()`

  #242 opened a year ago by stefan-dam
  1

• Issues with find.enrichment.py when I use the same IDs for study.txt and population.txt

  #273 opened 2 years ago by pomorale
  1

• Error in making result file

  #274 opened 2 years ago by Rhia15
  3

• Optimising go term tests

  #272 opened 2 years ago by francicco
  0

• What's the point of removing genes with identical identifiers?

  #271 opened 2 years ago by shelkmike
  0

• Information content of a custom GO annotation.

  #270 opened 2 years ago by ohdongha
  1

• Best practices for background gene sets

  #267 opened 2 years ago by stanleyjs
  3

• Different results when restricting background set to only include genes with at least one annotation term

  #259 opened 2 years ago by Maryam-Haghani
  1

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

  #263 opened 2 years ago by DylanSteinecke
  0

• Conditional tests?

  #264 opened 2 years ago by sjfleming
  0

• NOT FOUND IN DAG

  #246 opened 2 years ago by msheltra
  3

• p_value calculation with fisher_exact

  #262 opened 2 years ago by Maryam-Haghani
  2

• p-value calculation with fisher

  #261 opened 2 years ago by Maryam-Haghani
  0

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

  #260 opened 2 years ago by HelloWorldLTY
  0

• (Made a mistake)

  #257 opened 2 years ago by jasperhyp
  0

• How to get most recent common ancesters and shortest path distance between two terms?

  #256 opened 2 years ago by jasperhyp
  0

• Error: no population items seen in the annotations when using GAF file

  #254 opened 2 years ago by jlastoll
  1

• `log = None` cannot complete suppress stdout in GOEnrichmentStudyNS

  #238 opened 2 years ago by illumination-k
  2

• Output columns of grouped_gos

  #250 opened 2 years ago by cestaroa
  0

• Some questions about gene selection

  #249 opened 2 years ago by HelloWorldLTY
  0

• AttributeError: 'GOEnrichmentStudy' object has no attribute 'print_results'

  #248 opened 2 years ago by Liyong-Zhang
  0

• Error message while running goatools

  #247 opened 2 years ago by akaur1988
  0

• Discrepancies between using GoSearch and direct search on geneontology.org

  #243 opened 2 years ago by jasperhyp
  1

• Does gene ontology enrichment analysis work with Ensembl gene ids?

  #244 opened 2 years ago by BerkKilicoglu
  0

• Unhelpful Documentation, Missing High Level Interface

  #241 opened 3 years ago by fratajcz
  5

• cannot import name 'ncbi_tsv_to_py' from 'goatools.cli.ncbi_gene_results_to_python'

  #240 opened 3 years ago by jjacobsli
  0

• a couple of small issues with the readme

  #235 opened 3 years ago by yotamcons
  5

• download_ncbi_associations() fails while decompressing file

  #230 opened 3 years ago by msbentsen
  2

• Allow arbitrary letters in Aspect column

  #228 opened 3 years ago by serenalotreck
  2

• Incorrect data file for notebook : Run a Gene Ontology Enrichment Analysis (GOEA)

  #226 opened 3 years ago by vwongjun
  2