A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments.

ABSTRACT: 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).

SUBMITTER: Zhang S 

PROVIDER: S-EPMC8761752 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature