Basic4Cseq

Basic4Cseq is an R package that provides tools for processing and analyzing 4C-seq data. It filters, analyzes, and visualizes 4C-seq data using various functions. The package works by mapping short reads from a BAM file to a virtual fragment library and creating plots showing the coverage and contact profiles of the data. Users can export the data in Wig or CSV formats for further analysis and visualization.

Topic

Sequencing;Sequence analysis;Data visualisation

Detail

  • Operation: Sequence visualisation;Filtering

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.38.0

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Carolin Walter carolin.walter@uni-muenster.de

  • Collection: -

  • Maturity: -

Publications

  • Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.
  • Walter C, Schuetzmann D, Rosenbauer F, Dugas M. Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data. Bioinformatics. 2014 Nov 15;30(22):3268-9. doi: 10.1093/bioinformatics/btu497. Epub 2014 Jul 30. PMID: 25078398.
  • https://doi.org/10.1093/bioinformatics/btu497
  • PMID: 25078398
  • PMC: -

Download and documentation

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