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+
+
+# The `multiGSEA` `R` package
+
+## Authors
+
+Sebastian 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)
+
+## Introduction
+
+The `multiGSEA` package was designed to run a robust GSEA-based
+pathway enrichment for multiple omics layers. The enrichment is
+calculated for each omics layer separately and aggregated p-values are
+calculated afterwards to derive a composite multi-omics pathway
+enrichment.
+
+Pathway definitions can be downloaded from up to eight different
+pathway 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 the
+following ID formats:
+
+	* Entrez Gene ID
+	* Uniprot IDs
+	* Gene Symbols
+	* RefSeq
+	* Ensembl
+	
+Features 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 accomplished
+through the `metaboliteIDmapping` package.  This `AnnotationHub`
+package provides a comprehensive mapping table with more than one
+million compounds (`metaboliteIDmapping` on our [github
+page](https://github.com/yigbt/metaboliteIDmapping) or at
+[Bioconductor](http://bioconductor.org/packages/metaboliteIDmapping/)).
+  
+  
+## Installation
+
+There are two ways to install the `multiGSEA` package. For both you
+have to install and start R in at least version 4.0:
+
+(i) Use the Bioconductor framework:
+
+```R
+if (!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):
+
+```R
+install.packages("devtools")
+devtools::install_github("https://github.com/yigbt/multiGSEA")
+```
+
+Once installed, just load the `multiGSEA` package with:
+
+```R
+library(multiGSEA)
+```
+
+
+# Workflow
+
+A common workflow is exemplified in the package vignette and is
+typically 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
+[Bioconductor
+page](https://bioconductor.org/packages/release/bioc/vignettes/multiGSEA/inst/doc/multiGSEA.html).
+
+
+# LICENSE
+
+Copyright (C) 2011 - 2020 Helmholtz Centre for Environmental Research
+UFZ.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or (at
+your option) any later version.
+
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the UFZ
+License document for more details:
+<https://github.com/yigbt/multiGSEA/blob/master/LICENSE.md>