https://github.com/dvklopfenstein/enrichmentanalysis

Generic enrichment analysis
https://github.com/dvklopfenstein/enrichmentanalysis

benjamini-hochberg bonferroni enrichment-analysis fdr

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Generic enrichment analysis

• Host: GitHub
• URL: https://github.com/dvklopfenstein/enrichmentanalysis
• Owner: dvklopfenstein
• License: gpl-3.0
• Created: 2019-02-18T01:21:49.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2020-08-17T09:52:44.000Z (over 4 years ago)
• Last Synced: 2024-10-13T02:25:32.665Z (about 1 month ago)
• Topics: benjamini-hochberg, bonferroni, enrichment-analysis, fdr
• Language: Python
• Size: 718 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# Enrichment Analysis

[![PyPI version](/doc/images/badge_pypi.svg)](https://badge.fury.io/py/enrichmentanalysis-dvklopfenstein)

Do enrichment analysis on anything if you provide:

  * IDs of the population 

  * IDs of the study set

  * Associations between the IDs and the terms of interest

[Example data](https://github.com/dvklopfenstein/enrichmentanalysis/tree/master/data/exgo)

## The enrichment analysis steps performed by this repo's code

  1. Generate pvalues using Fishers exact test

  2. Do multipletest correction with any of SciPy's statsmodel functions:    

| multicorrect   | Description

|----------------|--------------------------------------

|`sm_bonferroni` | bonferroni one-step correction    

|`sm_sidak`      | sidak one-step correction    

|`sm_holm-sidak` | holm-sidak step-down method using Sidak adjustments    

|`sm_holm`       | holm step-down method using Bonferroni adjustments    

|`simes-hochberg`| simes-hochberg step-up method (independent)    

|`hommel`        | hommel closed method based on Simes tests (non-negative)    

|`fdr_bh`        | fdr correction with Benjamini/Hochberg (non-negative)    

|`fdr_by`        | fdr correction with Benjamini/Yekutieli (negative)    

|`fdr_tsbh`      | two stage fdr correction (non-negative)    

|`fdr_tsbky`     | two stage fdr correction (non-negative)    

## To Cite

This code is a generalized version of selected code from the [GOATOOLS](https://github.com/tanghaibao/goatools) repository,

which is used to run gene ontology enrichment analysis. 

### Citation

_Please cite the following research paper if you use this repo in your research_:

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

Copyright (C) 2016-2019, DV Klopfenstein. All rights reserved.