Titre
PascalX: a Python library for GWAS gene and pathway enrichment tests.
Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Krefl, D.
Auteure/Auteur
Brandulas Cammarata, A.
Auteure/Auteur
Bergmann, S.
Auteure/Auteur
Liens vers les personnes
Liens vers les unités
ISSN
1367-4811
Statut éditorial
Publié
Date de publication
2023-05-04
Volume
39
Numéro
5
Première page
btad296
Peer-reviewed
Oui
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
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/.
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/.
PID Serval
serval:BIB_D8824EBDC2F5
PMID
Open Access
Oui
Date de création
2023-05-08T09:00:16.698Z
Date de création dans IRIS
2025-07-19T04:43:36Z
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Nom
37137228_BIB_D8824EBDC2F5.pdf
Version du manuscrit
published
Licence
https://creativecommons.org/licenses/by/4.0
Taille
186.36 KB
Format
Adobe PDF
PID Serval
serval:BIB_D8824EBDC2F5.P001
URN
urn:nbn:ch:serval-BIB_D8824EBDC2F51
Somme de contrôle
(MD5):695e18084d7b7d64b9a56e6b80433a18