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

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 di

SUBMITTER: Denoulet M 

PROVIDER: S-EPMC9846423 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature