WhopGenome

WhopGenome is an R tool to process FASTA, VCF, and sequence alignment datasets. The whopGenome package includes an interface to access Bioconductor and gene ontology data from AmiGO and genome annotation from the University of California Santa Cruz (UCSC).

Topic

Sequence analysis;Data management

Detail

  • Operation: Data handling;Sequence alignment conversion;Genome annotation

  • Software interface: Library

  • Language: ;High-Speed Processing of VCF, FASTA and Alignment Data. Also provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO. It is capable to read, modify and write PLINK .PED-format pedigree files.;0.97;Library;R

  • License: GNU General Public License v2

  • Cost: Free

  • Version name: 0.9.7

  • Credit: -

  • Input: PLINK .PED-format pedigree

  • Output: -

  • Contact: Ulrich Wittelsbürger ulrich.wittelsbuerger@uni-duesseldorf.de, Martin J Lercher lercher@cs.uni-duesseldorf.de

  • Collection: -

  • Maturity: -

Publications

  • WhopGenome: high-speed access to whole-genome variation and sequence data in R.
  • Wittelsbürger U, Pfeifer B, Lercher MJ. WhopGenome: high-speed access to whole-genome variation and sequence data in R. Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636. Epub 2014 Oct 1. PMID: 25273104.
  • https://doi.org/10.1093/bioinformatics/btu636
  • PMID: 25273104
  • PMC: -

Download and documentation

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