{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T11:18:29Z","timestamp":1722683909691},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R\u2019s built-in I\/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.<\/jats:p>\n               <jats:p>Availability and implementation: The WhopGenome R package is available on CRAN at http:\/\/cran.r-project.org\/web\/packages\/WhopGenome\/ . A Bioconductor package has been submitted.<\/jats:p>\n               <jats:p>Contact: \u00a0lercher@cs.uni-duesseldorf.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu636","type":"journal-article","created":{"date-parts":[[2014,10,2]],"date-time":"2014-10-02T06:07:10Z","timestamp":1412230030000},"page":"413-415","source":"Crossref","is-referenced-by-count":2,"title":["WhopGenome: high-speed access to whole-genome variation and sequence data in R"],"prefix":"10.1093","volume":"31","author":[{"given":"Ulrich","family":"Wittelsb\u00fcrger","sequence":"first","affiliation":[{"name":"1 Institute for Computer Science, Heinrich Heine University, D-40255 D\u00fcsseldorf, Germany and 2 Cluster of Excellence on Plant Sciences CEPLAS, D-40255 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bastian","family":"Pfeifer","sequence":"additional","affiliation":[{"name":"1 Institute for Computer Science, Heinrich Heine University, D-40255 D\u00fcsseldorf, Germany and 2 Cluster of Excellence on Plant Sciences CEPLAS, D-40255 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin J.","family":"Lercher","sequence":"additional","affiliation":[{"name":"1 Institute for Computer Science, Heinrich Heine University, D-40255 D\u00fcsseldorf, Germany and 2 Cluster of Excellence on Plant Sciences CEPLAS, D-40255 D\u00fcsseldorf, Germany"},{"name":"1 Institute for Computer Science, Heinrich Heine University, D-40255 D\u00fcsseldorf, Germany and 2 Cluster of Excellence on Plant Sciences CEPLAS, D-40255 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,1]]},"reference":[{"key":"2023020116163631200_btu636-B1","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and samtools","volume":"25","author":"1000 Genome Project Data Processing Subgroup","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020116163631200_btu636-B2","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and vcftools","volume":"27","author":"1000 Genomes Project Analysis Group","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020116163631200_btu636-B3","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btn615","article-title":"Amigo: online access to ontology and annotation data","volume":"25","author":"Carbon","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020116163631200_btu636-B4","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023020116163631200_btu636-B5","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023020116163631200_btu636-B6","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1093\/bioinformatics\/btq671","article-title":"Tabix: fast retrieval of sequence features from generic tab-delimited files","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020116163631200_btu636-B7","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/btu168","article-title":"Variantannotation: a bioconductor package for exploration and annotation of genetic variants","volume":"30","author":"Obenchain","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020116163631200_btu636-B8","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1093\/molbev\/msu136","article-title":"Popgenome: an efficient swiss army knife for population genomic analyses in R","volume":"31","author":"Pfeifer","year":"2014","journal-title":"Mol. 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