goatools

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Hello, I am trying to do GOEnrichment analysis through goatools' GOEnrichmentStudy function. Everything works fine till I try to print out the enrichment results. Part of the code are as...

Liyong-Zhang

While running goatools, I get following error message. I am also attaching first 20 lines of my study, population and association file. Please help me with this. Thanks $ [20_lines_association.txt](https://github.com/tanghaibao/goatools/files/9199413/20_lines_association.txt)...

akaur1988

Error: Only few genes/proteins in the study are found in the background population.

6

I have been using GOA tools the latest zipped version, and getting the below error that only few input genes are in the background population. Is there a way to...

arumds

Discrepancies between using GoSearch and direct search on geneontology.org

1

Hi! Thanks for creating this wonderful library. I followed the instructions at https://github.com/tanghaibao/goatools/blob/main/notebooks/cell_cycle.ipynb to get GO-associated genes, but soon found out that there are some discrpancies between the results (in...

jasperhyp

Hello, I am trying to make goea by following the [notebook](https://github.com/tanghaibao/goatools/blob/main/notebooks/goea_nbt3102.ipynb) I wonder is it possible to do it with ensembl gene id as study genes?

BerkKilicoglu

Issue with `plot_gos()`

1

Hi there, I was trying to use `plot_gos()`, but I got an `FileNotFoundError`: > FileNotFoundError Traceback (most recent call last) > File ~/opt/anaconda3/envs/test/lib/python3.9/site-packages/pydot.py:1912, in Dot.create(self, prog, format, encoding) > 1911...

stefan-dam

Unhelpful Documentation, Missing High Level Interface

5

Hi! I really value your effort in trying to bring GOEA to python, but please, please, please go all the way. This whole library feels like someone did the hard...

fratajcz

Thanks for the helpful notebooks for downloading background gene sets. It seems like there is an issue with the ncbi tsv to py function. I am unable to call it...

jjacobsli

`log = None` cannot complete suppress stdout in GOEnrichmentStudyNS

2

Thanks for the great project! I want to stop logging completely, but `__init__` function in `GOEnrichmentStudy` has `print` regardless of `log` kwd, so I cannot. https://github.com/tanghaibao/goatools/blob/d3a63f9738efcdb9f2f49e40cf1fadeb58de9bac/goatools/go_enrichment.py#L256 I think if `log`...

illumination-k

Issues Generating Background GeneSet

1

I am trying to generate a background geneset for homo sapiens. I am currently trying to run GOATOOLS from jupyter notebook, but I am running into issues with the instructions...

TTCooper-PhD