UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C

MOTIVATION: UMI-4C, a technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI), is widely used to profile and quantitatively compare targeted chromosomal contact profiles. The analysis of UMI-4C experiments presents several computational challenges, includi...

Descripción completa

Detalles Bibliográficos
Autores principales: Ramos-Rodríguez, Mireia, Subirana-Granés, Marc, Pasquali, Lorenzo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502148/
https://www.ncbi.nlm.nih.gov/pubmed/34009302
http://dx.doi.org/10.1093/bioinformatics/btab392
Descripción
Sumario:MOTIVATION: UMI-4C, a technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI), is widely used to profile and quantitatively compare targeted chromosomal contact profiles. The analysis of UMI-4C experiments presents several computational challenges, including the removal of the PCR duplication bias and the identification of differential chromatin contacts. RESULTS: We have developed UMI4Cats (UMI-4C Analysis Turned Simple), an R package that facilitates processing, analyzing and visualizing of data obtained by UMI-4C experiments. AVAILABILITY AND IMPLEMENTATION: UMI4Cats is implemented as an R package supported on Linux, MacOS and MS Windows. UMI4Cats is available from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/UMI4Cats.html) and GitHub (https://github.com/Pasquali-lab/UMI4Cats). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ejemplares similares