From 6369bcc04cfcb1c7a8c77c2edec469854b87181c Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 13 Jun 2024 06:49:58 -0700 Subject: [PATCH 1/2] update README --- README.md | 46 ++++++++++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 4648a28..b217f61 100644 --- a/README.md +++ b/README.md @@ -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 +22,30 @@ | Email | | | 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) + +## Contents This package contains a Python library to @@ -66,26 +88,6 @@ 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 From 336f0738665d31d2264be66f6a388662622d6fe0 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 13 Jun 2024 07:04:04 -0700 Subject: [PATCH 2/2] add figure --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index b217f61..3d29156 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,8 @@ 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