{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T02:40:48Z","timestamp":1786156848649,"version":"3.56.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":662,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.<\/jats:p>\n               <jats:p>Availability and implementation: QuasR is implemented in R and C\/C++. Source code and binaries for major platforms (Linux, OS X and MS Windows) are available from Bioconductor (www.bioconductor.org\/packages\/release\/bioc\/html\/QuasR.html). The package includes a \u2018vignette\u2019 with step-by-step examples for typical work \ufb02ows.<\/jats:p>\n               <jats:p>Contact: \u00a0michael.stadler@fmi.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu781","type":"journal-article","created":{"date-parts":[[2014,11,23]],"date-time":"2014-11-23T01:09:29Z","timestamp":1416704969000},"page":"1130-1132","source":"Crossref","is-referenced-by-count":335,"title":["QuasR: quantification and annotation of short reads in R"],"prefix":"10.1093","volume":"31","author":[{"given":"Dimos","family":"Gaidatzis","sequence":"first","affiliation":[{"name":"1 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, 2Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and 3Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland"},{"name":"1 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, 2Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and 3Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Lerch","sequence":"additional","affiliation":[{"name":"1 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, 2Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and 3Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland"},{"name":"1 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, 2Swiss Institute of Bioinformatics, 4058 Basel, Switzerland and 3Novartis Institute for Biomedical Research, CH-4057 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Hahne","sequence":"additional","affiliation":[{"name":"1 Friedrich 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