A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments
Summary: Here, we present a quick-start protocol to perform generalized gene-set analysis of GWAS data on a metaset of gene lists generated by upstream pipelines, such as differential expression analysis, using the Multi-marker Analysis of GenoMic Annotation (MAGMA) software package and Hi-C coupled...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166721007899 |
| _version_ | 1831543232683573248 |
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| author | Siwei Zhang |
| author_facet | Siwei Zhang |
| author_sort | Siwei Zhang |
| collection | DOAJ |
| description | Summary: Here, we present a quick-start protocol to perform generalized gene-set analysis of GWAS data on a metaset of gene lists generated by upstream pipelines, such as differential expression analysis, using the Multi-marker Analysis of GenoMic Annotation (MAGMA) software package and Hi-C coupled H-MAGMA annotation data (de Leeuw et al., 2015; Sey et al., 2020). We specifically tailor the steps and operations to meet the multithreading capability in modern computers, a feature nowadays shared by personal computers and high-performance clusters alike.For complete details on the use and execution of this profile, please refer to Yao et al. (2021). |
| first_indexed | 2024-12-17T00:48:07Z |
| format | Article |
| id | doaj.art-6544e4a49b4c47ec89544bfa8372b3df |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-17T00:48:07Z |
| publishDate | 2022-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-6544e4a49b4c47ec89544bfa8372b3df2022-12-21T22:09:50ZengElsevierSTAR Protocols2666-16672022-03-0131101083A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environmentsSiwei Zhang0Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL 60637, USA; Corresponding authorSummary: Here, we present a quick-start protocol to perform generalized gene-set analysis of GWAS data on a metaset of gene lists generated by upstream pipelines, such as differential expression analysis, using the Multi-marker Analysis of GenoMic Annotation (MAGMA) software package and Hi-C coupled H-MAGMA annotation data (de Leeuw et al., 2015; Sey et al., 2020). We specifically tailor the steps and operations to meet the multithreading capability in modern computers, a feature nowadays shared by personal computers and high-performance clusters alike.For complete details on the use and execution of this profile, please refer to Yao et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166721007899BioinformaticsGeneticsGenomicsNeuroscience |
| spellingShingle | Siwei Zhang A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments STAR Protocols Bioinformatics Genetics Genomics Neuroscience |
| title | A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments |
| title_full | A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments |
| title_fullStr | A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments |
| title_full_unstemmed | A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments |
| title_short | A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments |
| title_sort | simplified protocol for performing magma h magma gene set analysis utilizing high performance computing environments |
| topic | Bioinformatics Genetics Genomics Neuroscience |
| url | http://www.sciencedirect.com/science/article/pii/S2666166721007899 |
| work_keys_str_mv | AT siweizhang asimplifiedprotocolforperformingmagmahmagmagenesetanalysisutilizinghighperformancecomputingenvironments AT siweizhang simplifiedprotocolforperformingmagmahmagmagenesetanalysisutilizinghighperformancecomputingenvironments |