A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments.
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ABSTRACT:
SUBMITTER: Zhang S
PROVIDER: S-EPMC8761752 | biostudies-literature | 2022 Mar
REPOSITORIES: biostudies-literature
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A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments.
STAR protocols 20220111 1
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 perso ...[more]
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