From b47565450979a95f7416dafc70d3be1e14f33c4d Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 18 Nov 2024 20:34:44 +0100 Subject: [PATCH 1/4] Polish NEWS --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/NEWS.md b/NEWS.md index f13c574..b408af3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# mulea 1.1.1 + +- Updated citation to the BMC Bioinformatics article. + # mulea 1.1.0 ## Minor Improvements From 2fb99c9a7736b308f95f72a7655cda54ce20a12d Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Tue, 19 Nov 2024 09:32:10 +0100 Subject: [PATCH 2/4] Bump version in DESCRIPTION file --- DESCRIPTION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3601914..373f9c7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,7 @@ Package: mulea Type: Package Title: Enrichment Analysis Using Multiple Ontologies and False Discovery Rate -Version: 1.1.0 -Date: 2024-09-24 +Version: 1.1.1 Authors@R: c( person("Cezary", "Turek", role = "aut", comment = c(ORCID = "0000-0002-1445-5378")), From b29ee78e350fda1ac920041caa8421e4469c1031 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Tue, 19 Nov 2024 09:32:25 +0100 Subject: [PATCH 3/4] Update codemeta --- codemeta.json | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/codemeta.json b/codemeta.json index 7fed116..de768dd 100644 --- a/codemeta.json +++ b/codemeta.json @@ -2,18 +2,24 @@ "@context": "https://doi.org/10.5063/schema/codemeta-2.0", "@type": "SoftwareSourceCode", "identifier": "mulea", - "description": "Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs an innovative empirical false discovery rate (eFDR) correction method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. Beyond conventional tools, mulea incorporates a wide range of ontologies encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility empowers researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardized GMT format) for 27 model organisms, covering 16 databases and various identifiers. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these 879 pre-defined ontologies. Furthermore, mulea's architecture allows for easy integration of user-defined ontologies, expanding its applicability across diverse research areas.", - "name": "mulea: Enrichment Analysis using Multiple Ontologies and FDR Correction", + "description": "Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.", + "name": "mulea: Enrichment Analysis Using Multiple Ontologies and False Discovery Rate", "codeRepository": "https://github.com/ELTEbioinformatics/mulea", "issueTracker": "https://github.com/ELTEbioinformatics/mulea/issues", "license": "https://spdx.org/licenses/GPL-2.0", - "version": "0.99.12", + "version": "1.1.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.4.0 (2024-04-24)", + "runtimePlatform": "R version 4.2.2 Patched (2022-11-10 r83330)", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, "author": [ { "@type": "Person", @@ -354,7 +360,7 @@ }, "SystemRequirements": null }, - "fileSize": "6596.712KB", + "fileSize": "6767.184KB", "citation": [ { "@type": "ScholarlyArticle", @@ -411,17 +417,17 @@ "familyName": "Ari" } ], - "name": "mulea - an R package for enrichment analysis using multiple \n ontologies and empirical FDR correction.", - "identifier": "10.1101/2024.02.28.582444v1", - "url": "https://doi.org/10.1101/2024.02.28.582444", - "@id": "https://doi.org/10.1101/2024.02.28.582444v1", - "sameAs": "https://doi.org/10.1101/2024.02.28.582444v1", + "name": "mulea - an R package for enrichment analysis using multiple \n ontologies and empirical false discovery rate.", + "url": "https://doi.org/10.1186/s12859-024-05948-7", + "pagination": "334", "isPartOf": { "@type": "PublicationIssue", + "issueNumber": "1", "datePublished": "2024", "isPartOf": { "@type": ["PublicationVolume", "Periodical"], - "name": "bioRxiv" + "volumeNumber": "25", + "name": "BMC Bioinformatics" } } } From da62580c286dfa4a31a69b21131abba381feed60 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Tue, 19 Nov 2024 09:32:35 +0100 Subject: [PATCH 4/4] Update CRAN comments --- cran-comments.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cran-comments.md b/cran-comments.md index e5d362d..174947e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,7 @@ +# mulea 1.1.1 + +Issues with earlier submissions are still there, no new issues. + # mulea 1.0.1 0 errors | 0 warnings | 1 note