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dc.contributor.authorHaberle, Vanja
dc.contributor.authorForrest, Alistair R.R.
dc.contributor.authorHayashizaki, Yoshihide
dc.contributor.authorCarninci, Piero
dc.contributor.authorLenhard, Boris
dc.PublishedNucleic Acids Research 2015, 43(8:e51)eng
dc.description.abstractCap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high resolution and functional significance, published CAGE data are still underused in promoter analysis due to the absence of tools that enable its efficient manipulation and integration with other genome data types. Here we present CAGEr, an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform. Crucially, we provide collections of TSSs derived from most published CAGE datasets, as well as direct access to FANTOM5 resource of TSSs for numerous human and mouse cell/tissue types from within R, greatly increasing the accessibility of precise context-specific TSS data for integrative analyses. The CAGEr package is freely available from Bioconductor at
dc.publisherOxford University Pressen_US
dc.relation.ispartof<a href="" target="_blank">Overlapping transcription initiation codes and promoter interpretation in vertebrate development and differentiation</a>en_US
dc.rightsAttribution CC BYeng
dc.titleCAGEr: Precise TSS data retrieval and high-resolution promoterome mining for integrative analysesen_US
dc.typePeer reviewed
dc.typeJournal article
dc.rights.holderCopyright 2015 The Authorsen_US
dc.subject.nsiVDP::Matematikk og naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475
dc.subject.nsiVDP::Mathematics and natural scienses: 400::Basic biosciences: 470::Bioinformatics: 475

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