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4 mai 2023
- doi: 10.1093/bioinformatics/btad296
- issn: 1367-4803
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info:eu-repo/semantics/altIdentifier/pmid/37137228
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info:eu-repo/semantics/altIdentifier/eissn/1367-4811
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info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_D8824EBDC2F51
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Mots-clés
Genome-Wide Association Study; Gene Library; Software; Polymorphism, Single Nucleotide; LibrariesSujets proches
Tools Examples Exemplars Statistical data Cases, clinical reports, statistics Units of inheritance Units of heredity Hand tools Handtools Tally sticks Scores Notched sticks Statistical data Statistical analysis Statistical methods Statistical science Group dynamics Association Groups, Social Chance variables Stochastic variables Pattern Model Competitive examinations Tests Idioms, corrections, errorsCiter ce document
D. Krefl et al., « PascalX: a Python library for GWAS gene and pathway enrichment tests. », Serveur académique Lausannois, ID : 10.1093/bioinformatics/btad296
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Résumé
'PascalX' is a Python library providing fast and accurate tools for mapping SNP-wise GWAS summary statistics. Specifically, it allows for scoring genes and annotated gene sets for enrichment signals based on data from, both, single GWAS and pairs of GWAS. The gene scores take into account the correlation pattern between SNPs. They are based on the cumulative density function of a linear combination of χ2 distributed random variables, which can be calculated either approximately or exactly to high precision. Acceleration via multithreading and GPU is supported. The code of PascalX is fully open source and well suited as a base for method development in the GWAS enrichment test context. The source code is available at https://github.com/BergmannLab/PascalX and archived under doi://10.5281/zenodo.4429922. A user manual with usage examples is available at https://bergmannlab.github.io/PascalX/.
