{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T12:40:38Z","timestamp":1713876038033},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: High-throughput sequencing has become an essential experimental approach for the investigation of transcriptional mechanisms. For some applications like ChIP-seq, several approaches for the prediction of peak locations exist. However, these methods are not designed for the identification of transcription start sites (TSSs) because such datasets contain qualitatively different noise.<\/jats:p><jats:p>In this application note, the R package TSSi is presented which provides a heuristic framework for the identification of TSSs based on 5\u2032 mRNA tag data. Probabilistic assumptions for the distribution of the data, i.e. for the observed positions of the mapped reads, as well as for systematic errors, i.e. for reads which map closely but not exactly to a real TSS, are made and can be adapted by the user. The framework also comprises a regularization procedure which can be applied as a preprocessing step to decrease the noise and thereby reduce the number of false predictions.<\/jats:p><jats:p>Availability: The R package TSSi is available from the Bioconductor web site: www.bioconductor.org\/packages\/release\/bioc\/html\/TSSi.html.<\/jats:p><jats:p>Contact: \u00a0ckreutz@fdm.uni-freiburg.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts189","type":"journal-article","created":{"date-parts":[[2012,4,19]],"date-time":"2012-04-19T00:25:22Z","timestamp":1334795122000},"page":"1641-1642","source":"Crossref","is-referenced-by-count":0,"title":["TSSi\u2014an R package for transcription start site identification from 5\u2032 mRNA tag data"],"prefix":"10.1093","volume":"28","author":[{"given":"C.","family":"Kreutz","sequence":"first","affiliation":[{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"}]},{"given":"J. S.","family":"Gehring","sequence":"additional","affiliation":[{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"}]},{"given":"D.","family":"Lang","sequence":"additional","affiliation":[{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"}]},{"given":"R.","family":"Reski","sequence":"additional","affiliation":[{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"}]},{"given":"J.","family":"Timmer","sequence":"additional","affiliation":[{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"},{"name":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"}]},{"given":"S. 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