UMI4Cats

'UMI4Cats' is an R package for analyzing UMI-4C (Unique Molecular Identifiers - Chromosome Conformation Capture) experiments. UMI-4C is a technique that combines chromosome conformation capture (4C) with unique molecular identifiers (UMI) to profile and quantitatively compare targeted chromosomal contact profiles. The computational challenges in UMI-4C analysis, such as PCR duplication bias removal and identification of differential chromatin contacts, are addressed by UMI4Cats. This package provides functionalities for processing, analyzing, and visualizing UMI-4C data.

Topic

Chromosome conformation capture;Proteomics experiment;DNA;Sequencing

Detail

  • Operation: Visualisation;Quantification;Standardisation and normalisation

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: Spanish Ministry of Economy and Competiveness , EFSD/JDRF/Lilly Programme on Type 1 Diabetes Research, ‘Unidad de Excelencia Maria de Maeztu’, Premi Gonçal Lloveras i Vallès a l’Excelència en Investigació junior 2020.

  • Input: -

  • Output: -

  • Contact: Mireia Ramos-Rodriguez mireiarr9@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C.
  • Ramos-Rodríguez M, et al. UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C. UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C. 2021; 37:4240-4242. doi: 10.1093/bioinformatics/btab392
  • https://doi.org/10.1093/BIOINFORMATICS/BTAB392
  • PMID: 34009302
  • PMC: PMC9502148

Download and documentation

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