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48 changes: 26 additions & 22 deletions README.md
Original file line number Diff line number Diff line change
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# Tools for Gene Ontology

[![DOI](/doc/images/DOI.svg)](https://www.nature.com/articles/s41598-018-28948-z)
[![Latest PyPI version](https://img.shields.io/pypi/v/goatools.svg)](https://pypi.python.org/pypi/goatools)
[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
[![Github Actions](https://github.com/tanghaibao/goatools/workflows/build/badge.svg)](https://github.com/tanghaibao/goatools/actions)
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| Email | <[email protected]> |
| License | BSD |

## Description
## How to cite

> [!TIP]
> GOATOOLS is now published in Scientific Reports!
>
> _Klopfenstein DV, ... Tang H (2018) GOATOOLS: A Python library for Gene
> Ontology analyses [Scientific reports](https://www.nature.com/articles/s41598-018-28948-z)_
- **GO Grouping**:
Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
A detailed description of GOATOOLS GO grouping is found in the
[manuscript](https://www.nature.com/articles/s41598-018-28948-z).
- **Compare GO lists**:
Compare [two](https://github.com/tanghaibao/goatools/issues/162) or more lists
of GO IDs using `compare_gos.py`, which can be used with or without
grouping.
- **Stochastic GOEA simulations**:
One of the findings resulting from our simulations is:
[Larger study sizes result in higher GOEA sensitivity](https://github.com/dvklopfenstein/goatools_simulation#manuscript-figures),
meaning fewer truly significant observations go unreported.
The code for the stochastic GOEA simulations
described in the paper is found [here](https://github.com/dvklopfenstein/goatools_simulation)

![GOATOOLS example](https://www.dropbox.com/scl/fi/m6c3ckv1vzj3tgy31b1l4/41598_2018_28948_Fig2_HTML.png?rlkey=ud8n05c1dcejtg32z6jy2m4lt&raw=1)

## Contents

This package contains a Python library to

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GO terms) to GOslim terms (analog to the map2slim.pl script supplied
by geneontology.org)

## To Cite

Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H [GOATOOLS: A Python library for Gene Ontology analyses](https://www.nature.com/articles/s41598-018-28948-z)
_Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z

- **GO Grouping**:
Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
A detailed description of GOATOOLS GO grouping is found in the
[manuscript](https://www.nature.com/articles/s41598-018-28948-z).
- **Compare GO lists**:
Compare [two](https://github.com/tanghaibao/goatools/issues/162) or more lists
of GO IDs using `compare_gos.py`, which can be used with or without
grouping.
- **Stochastic GOEA simulations**:
One of the findings resulting from our simulations is:
[Larger study sizes result in higher GOEA sensitivity](https://github.com/dvklopfenstein/goatools_simulation#manuscript-figures),
meaning fewer truly significant observations go unreported.
The code for the stochastic GOEA simulations
described in the paper is found [here](https://github.com/dvklopfenstein/goatools_simulation)

## Installation

Make sure your Python version >= 3.7, and download an
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