Titre :

ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR

Auteur(s) :

Denoulet, Marie [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Université de Lille
Brulé, Mathilde [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Université de Lille
Anquez, François [Auteur]
Institut pour la recherche sur le cancer de Lille [Lille] [IRCL]
Vincent, Audrey [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Schnipper, Julie [Auteur]
Laboratoire de Physiologie Cellulaire et Moléculaire - UR UPJV 4667 [LPCM]
Adriaenssens, Eric [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Toillon, Robert-Alain [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Le Bourhis, Xuefen [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Lagadec, Chann [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Université de Lille

Titre de la revue :

Bioinformatics

Éditeur :

Oxford University Press (OUP)

Date de publication :

2023-01-11

ISSN :

1367-4803

Discipline(s) HAL :

Sciences du Vivant [q-bio]/Médecine humaine et pathologie

Résumé en anglais : [en]

Abstract Motivation Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare ...
Lire la suite >Abstract Motivation Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the Bisulfite Sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task. Results Here, we implement a new R-based tool, called ABSP for Analysis of Bisulfite Sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps, and generates publication-ready graphics. Availability and implementation The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP. Supplementary information Supplementary data are available at Bioinformatics online.Lire moins >

Langue :

Anglais

Vulgarisation :

Non

Collections :

• Centre d'Infection et d'Immunité de Lille (CIIL) - U1019 - UMR 9017

Source :

Harvested from HAL

Date de dépôt :

2024-02-17T03:39:01Z