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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>

	a/README.md		b/README.md
1	<!-- badges: start -->	1
2	[![R-CMD-check](https://github.com/yigbt/multiGSEA/actions/workflows/test.yaml/badge.svg)](https://github.com/yigbt/multiGSEA/actions/workflows/test.yaml)
3	<!-- badges: end -->
4
5
6	# The `multiGSEA` `R` package	2	# The `multiGSEA` `R` package
7		3
8	## Authors	4	## Authors
9		5
10	Sebastian Canzler and Jörg Hackermüller	6	Sebastian Canzler and Jörg Hackermüller
11		7
12	[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)	8	[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)
13		9
14	## Introduction	10	## Introduction
15		11
16	The `multiGSEA` package was designed to run a robust GSEA-based	12	The `multiGSEA` package was designed to run a robust GSEA-based
17	pathway enrichment for multiple omics layers. The enrichment is	13	pathway enrichment for multiple omics layers. The enrichment is
18	calculated for each omics layer separately and aggregated p-values are	14	calculated for each omics layer separately and aggregated p-values are
19	calculated afterwards to derive a composite multi-omics pathway	15	calculated afterwards to derive a composite multi-omics pathway
20	enrichment.	16	enrichment.
21		17
22	Pathway definitions can be downloaded from up to eight different	18	Pathway definitions can be downloaded from up to eight different
23	pathway databases by means of the	19	pathway databases by means of the
24	[`graphite`](http://bioconductor.org/packages/release/bioc/html/graphite.html)	20	[`graphite`](http://bioconductor.org/packages/release/bioc/html/graphite.html)
25	Bioconductor package.	21	Bioconductor package.
26		22
27	Features of the transcriptome and proteome level can be mapped to the	23	Features of the transcriptome and proteome level can be mapped to the
28	following ID formats:	24	following ID formats:
29		25
30	* Entrez Gene ID	26	* Entrez Gene ID
31	* Uniprot IDs	27	* Uniprot IDs
32	* Gene Symbols	28	* Gene Symbols
33	* RefSeq	29	* RefSeq
34	* Ensembl	30	* Ensembl
35		31
36	Features of the metabolome layer can be mapped to:	32	Features of the metabolome layer can be mapped to:
37		33
38	* Comptox Dashboard IDs (DTXCID, DTXSID)	34	* Comptox Dashboard IDs (DTXCID, DTXSID)
39	* CAS-RN numbers	35	* CAS-RN numbers
40	* Pubchem IDs (CID)	36	* Pubchem IDs (CID)
41	* HMDB IDs	37	* HMDB IDs
42	* KEGG IDs	38	* KEGG IDs
43	* ChEBI IDs	39	* ChEBI IDs
44	* Drugbank IDs	40	* Drugbank IDs
45	* Common names	41	* Common names
46		42
47		43
48	Please note, that the mapping of metabolite IDs is accomplished	44	Please note, that the mapping of metabolite IDs is accomplished
49	through the `metaboliteIDmapping` package. This `AnnotationHub`	45	through the `metaboliteIDmapping` package. This `AnnotationHub`
50	package provides a comprehensive mapping table with more than one	46	package provides a comprehensive mapping table with more than one
51	million compounds (`metaboliteIDmapping` on our [github	47	million compounds (`metaboliteIDmapping` on our [github
52	page](https://github.com/yigbt/metaboliteIDmapping) or at	48	page](https://github.com/yigbt/metaboliteIDmapping) or at
53	[Bioconductor](http://bioconductor.org/packages/metaboliteIDmapping/)).	49	[Bioconductor](http://bioconductor.org/packages/metaboliteIDmapping/)).
54		50
55		51
56	## Installation	52	## Installation
57		53
58	There are two ways to install the `multiGSEA` package. For both you	54	There are two ways to install the `multiGSEA` package. For both you
59	have to install and start R in at least version 4.0:	55	have to install and start R in at least version 4.0:
60		56
61	(i) Use the Bioconductor framework:	57	(i) Use the Bioconductor framework:
62		58
63	```R	59	```R
64	if (!requireNamespace("BiocManager", quietly = TRUE))	60	if (!requireNamespace("BiocManager", quietly = TRUE))
65	install.packages("BiocManager")	61	install.packages("BiocManager")
66		62
67	BiocManager::install("multiGSEA")	63	BiocManager::install("multiGSEA")
68	```	64	```
69		65
70	(ii) Alternatively, you can install the most up to date version	66	(ii) Alternatively, you can install the most up to date version
71	(development) easily with	67	(development) easily with
72	[devtools](https://github.com/hadley/devtools):	68	[devtools](https://github.com/hadley/devtools):
73		69
74	```R	70	```R
75	install.packages("devtools")	71	install.packages("devtools")
76	devtools::install_github("https://github.com/yigbt/multiGSEA")	72	devtools::install_github("https://github.com/yigbt/multiGSEA")
77	```	73	```
78		74
79	Once installed, just load the `multiGSEA` package with:	75	Once installed, just load the `multiGSEA` package with:
80		76
81	```R	77	```R
82	library(multiGSEA)	78	library(multiGSEA)
83	```	79	```
84		80
85		81
86	# Workflow	82	# Workflow
87		83
88	A common workflow is exemplified in the package vignette and is	84	A common workflow is exemplified in the package vignette and is
89	typically separated in the following steps:	85	typically separated in the following steps:
90		86
91	1. Load required libraries, including the `multiGSEA` package, and	87	1. Load required libraries, including the `multiGSEA` package, and
92	omics data sets.	88	omics data sets.
93	2. Create data structure for enrichment analysis.	89	2. Create data structure for enrichment analysis.
94	3. Download and customize the pathway definitions.	90	3. Download and customize the pathway definitions.
95	4. Run the pathway enrichment for each omics layer.	91	4. Run the pathway enrichment for each omics layer.
96	5. Calculate the aggregated pathway enrichment.	92	5. Calculate the aggregated pathway enrichment.
97		93
98		94
99	For more information please have a look in the vignette at our	95	For more information please have a look in the vignette at our
100	[Bioconductor	96	[Bioconductor
101	page](https://bioconductor.org/packages/release/bioc/vignettes/multiGSEA/inst/doc/multiGSEA.html).	97	page](https://bioconductor.org/packages/release/bioc/vignettes/multiGSEA/inst/doc/multiGSEA.html).
102		98
103		99
104	# LICENSE	100	# LICENSE
105		101
106	Copyright (C) 2011 - 2020 Helmholtz Centre for Environmental Research	102	Copyright (C) 2011 - 2020 Helmholtz Centre for Environmental Research
107	UFZ.	103	UFZ.
108		104
109	This program is free software: you can redistribute it and/or modify	105	This program is free software: you can redistribute it and/or modify
110	it under the terms of the GNU General Public License as published by	106	it under the terms of the GNU General Public License as published by
111	the Free Software Foundation, either version 3 of the License, or (at	107	the Free Software Foundation, either version 3 of the License, or (at
112	your option) any later version.	108	your option) any later version.
113		109
114	This program is distributed in the hope that it will be useful, but	110	This program is distributed in the hope that it will be useful, but
115	WITHOUT ANY WARRANTY; without even the implied warranty of	111	WITHOUT ANY WARRANTY; without even the implied warranty of
116	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the UFZ	112	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the UFZ
117	License document for more details:	113	License document for more details:
118	<https://github.com/yigbt/multiGSEA/blob/master/LICENSE.md>	114	<https://github.com/yigbt/multiGSEA/blob/master/LICENSE.md>