{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T07:53:50Z","timestamp":1771660430748,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Basic4Cseq is an R\/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. The package processes aligned 4C-seq raw data stored in binary alignment\/map (BAM) format and maps the short reads to a corresponding virtual fragment library. Functions are included to create virtual fragment libraries providing chromosome position and further information on 4C-seq fragments (length and uniqueness of the fragment ends, and blindness of a fragment) for any BSGenome package. An optional filter is included for BAM files to remove invalid 4C-seq reads, and further filter functions are offered for 4C-seq fragments. Additionally, basic quality controls based on the read distribution are included. Fragment data in the vicinity of the experiment\u2019s viewpoint are visualized as coverage plot based on a running median approach and a multi-scale contact profile. Wig files or csv files of the fragment data can be exported for further analyses and visualizations of interactions with other programs.<\/jats:p>\n               <jats:p>Availability and implementation: Basic4Cseq is implemented in R and available at http:\/\/www.bioconductor.org\/ . A vignette with detailed descriptions of the functions is included in the package.<\/jats:p>\n               <jats:p>Contact: \u00a0Carolin.Walter@uni-muenster.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu497","type":"journal-article","created":{"date-parts":[[2014,7,31]],"date-time":"2014-07-31T03:29:43Z","timestamp":1406777383000},"page":"3268-3269","source":"Crossref","is-referenced-by-count":19,"title":["Basic4Cseq: an R\/Bioconductor package for analyzing 4C-seq data"],"prefix":"10.1093","volume":"30","author":[{"given":"Carolin","family":"Walter","sequence":"first","affiliation":[{"name":"1 Institute of Medical Informatics, University of M\u00fcnster, 48149 M\u00fcnster, Germany, and 2 Institute of Molecular Tumorbiology, University of M\u00fcnster, 48149 M\u00fcnster, Germany"}]},{"given":"Daniel","family":"Schuetzmann","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Informatics, University of M\u00fcnster, 48149 M\u00fcnster, Germany, and 2 Institute of Molecular Tumorbiology, University of M\u00fcnster, 48149 M\u00fcnster, Germany"}]},{"given":"Frank","family":"Rosenbauer","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Informatics, University of M\u00fcnster, 48149 M\u00fcnster, Germany, and 2 Institute of Molecular Tumorbiology, University of M\u00fcnster, 48149 M\u00fcnster, Germany"}]},{"given":"Martin","family":"Dugas","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Informatics, University of M\u00fcnster, 48149 M\u00fcnster, Germany, and 2 Institute of Molecular Tumorbiology, University of M\u00fcnster, 48149 M\u00fcnster, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,7,30]]},"reference":[{"key":"2023012712002728900_btu497-B1","first-page":"212","article-title":"Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4c-seq) method","volume":"786","author":"Gheldof","year":"2012","journal-title":"Methods Mol. 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