README.md
<!-- badges: start --> [](https://github.com/yigbt/multiGSEA/actions/workflows/test.yaml) <!-- badges: end --># The `multiGSEA` `R` package## AuthorsSebastian Canzler and Jörg Hackermüller[multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data](https://doi.org/10.1186/s12859-020-03910-x), _BMC Bioinformatics_ 21, 561 (2020)## IntroductionThe `multiGSEA` package was designed to run a robust GSEA-basedpathway enrichment for multiple omics layers. The enrichment iscalculated for each omics layer separately and aggregated p-values arecalculated afterwards to derive a composite multi-omics pathwayenrichment.Pathway definitions can be downloaded from up to eight differentpathway databases by means of the[`graphite`](http://bioconductor.org/packages/release/bioc/html/graphite.html)Bioconductor package.Features of the transcriptome and proteome level can be mapped to thefollowing ID formats:* Entrez Gene ID* Uniprot IDs* Gene Symbols* RefSeq* EnsemblFeatures of the metabolome layer can be mapped to:* Comptox Dashboard IDs (DTXCID, DTXSID)* CAS-RN numbers* Pubchem IDs (CID)* HMDB IDs* KEGG IDs* ChEBI IDs* Drugbank IDs* Common names Please note, that the mapping of metabolite IDs is accomplishedthrough the `metaboliteIDmapping` package. This `AnnotationHub`package provides a comprehensive mapping table with more than onemillion compounds (`metaboliteIDmapping` on our [githubpage](https://github.com/yigbt/metaboliteIDmapping) or at[Bioconductor](http://bioconductor.org/packages/metaboliteIDmapping/)). ## InstallationThere are two ways to install the `multiGSEA` package. For both youhave to install and start R in at least version 4.0:(i) Use the Bioconductor framework:```Rif (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("multiGSEA")```(ii) Alternatively, you can install the most up to date version(development) easily with[devtools](https://github.com/hadley/devtools):```Rinstall.packages("devtools")devtools::install_github("https://github.com/yigbt/multiGSEA")```Once installed, just load the `multiGSEA` package with:```Rlibrary(multiGSEA)```# WorkflowA common workflow is exemplified in the package vignette and istypically separated in the following steps:1. Load required libraries, including the `multiGSEA` package, and omics data sets.2. Create data structure for enrichment analysis.3. Download and customize the pathway definitions.4. Run the pathway enrichment for each omics layer.5. Calculate the aggregated pathway enrichment.For more information please have a look in the vignette at our[Bioconductorpage](https://bioconductor.org/packages/release/bioc/vignettes/multiGSEA/inst/doc/multiGSEA.html).# LICENSECopyright (C) 2011 - 2020 Helmholtz Centre for Environmental ResearchUFZ.This program is free software: you can redistribute it and/or modifyit under the terms of the GNU General Public License as published bythe Free Software Foundation, either version 3 of the License, or (atyour option) any later version.This program is distributed in the hope that it will be useful, butWITHOUT ANY WARRANTY; without even the implied warranty ofMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the UFZLicense document for more details:<https://github.com/yigbt/multiGSEA/blob/master/LICENSE.md>
