Merge pull request #5833 from bernt-matthias/multigsea-reference

Add missing reference to MultiGSEA tutorial
galaxyproject · Mar 11, 2025 · d29ede7 · d29ede7
2 parents 6054cbe + 72c977c
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diff --git a/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.bib b/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.bib
@@ -45,4 +45,15 @@ @article{LOUGHIN2004467
 issn = {0167-9473},
 doi = {10.1016/j.csda.2003.11.020},
 author = {Thomas M. Loughin}
+}
+
+@article{Canzler2020,
+  title={multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data},
+  author={Canzler, Sebastian and Hackerm{\"u}ller, J{\"o}rg},
+  journal={BMC bioinformatics},
+  volume={21},
+  pages={1--13},
+  year={2020},
+  publisher={Springer},
+  doi = {10.1186/s12859-020-03910-x}
 }
diff --git a/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.md b/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.md
@@ -27,7 +27,7 @@ contributions:
 ---
 
 
-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.
+The multiGSEA package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers (Canzler and Hackermüller, 2020) {% cite Canzler2020 %}. 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 Bioconductor package (Sales, Calura, and Romualdi 2018). Feature mapping for transcripts and proteins is supported towards Entrez Gene IDs, Uniprot, Gene Symbol, RefSeq, and Ensembl IDs. The mapping is accomplished through the AnnotationDbi package (Pagès et al. 2019) and currently supported for 11 different model organisms including human, mouse, and rat. ID conversion of metabolite features to Comptox Dashboard IDs (DTXCID, DTXSID), CAS-numbers, Pubchem IDs (CID), HMDB, KEGG, ChEBI, Drugbank IDs, or common metabolite names is accomplished through the AnnotationHub package metabliteIDmapping. This package provides a comprehensive ID mapping for more than 1.1 million entries.
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@@ Expand Up / @@ -27,7 +27,7 @@ contributions: @@
     ---
-    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.
+    The multiGSEA package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers (Canzler and Hackermüller, 2020) {% cite Canzler2020 %}. 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 Bioconductor package (Sales, Calura, and Romualdi 2018). Feature mapping for transcripts and proteins is supported towards Entrez Gene IDs, Uniprot, Gene Symbol, RefSeq, and Ensembl IDs. The mapping is accomplished through the AnnotationDbi package (Pagès et al. 2019) and currently supported for 11 different model organisms including human, mouse, and rat. ID conversion of metabolite features to Comptox Dashboard IDs (DTXCID, DTXSID), CAS-numbers, Pubchem IDs (CID), HMDB, KEGG, ChEBI, Drugbank IDs, or common metabolite names is accomplished through the AnnotationHub package metabliteIDmapping. This package provides a comprehensive ID mapping for more than 1.1 million entries.
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