-
Notifications
You must be signed in to change notification settings - Fork 210
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Showing
1 changed file
with
26 additions
and
22 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,6 +1,5 @@ | ||
# 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) | ||
|
@@ -23,7 +22,32 @@ | |
| 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 | ||
|
||
|
@@ -66,26 +90,6 @@ This package contains a Python library to | |
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 | ||
|