riboSeqR specifications


Unique identifier OMICS_12937
Name riboSeqR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.14.0
Stability Stable
methods, BiocGenerics, IRanges, GenomicRanges, Rsamtools, GenomeInfoDb, BiocStyle, seqLogo, RUnit, abind, baySeq, R(>=3.0.2)
Maintained Yes




No version available



  • person_outline Thomas J. Hardcastle
  • person_outline Betty Chung
  • person_outline Ian Brierley

Publication for riboSeqR

riboSeqR citations


Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS targeting

PMCID: 5662147
PMID: 28970560
DOI: 10.1038/s41477-017-0024-6

[…] l. 2016.Our subsequent analysis differentiated mRNAs with miRNA targets in the 5’ UTR, CDS and 3’ UTR from those without targets. The CDS regions were defined by the R software Bioconductor package – riboSeqR - that utilizes the triplet periodicity of ribosome profiling for the de novo inference of AUG-initiated coding sequences that are supported by RPFs and we used the seed-sequence rule to iden […]


Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

Nucleic Acids Res
PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] ned to the genomes of a dozen of organisms and RiboGalaxy () allows researchers to analyse their data on a cloud server via an internet browser using a variety of tools from such packages as RUST (), riboSeqR () and RiboTools (). Publicly available RiboSeq data also can be accessed at RPFdb (). Furthermore, sORFs.org () collects ORFs whose translation is supported with RiboSeq data, and TISdb () i […]

riboSeqR institution(s)
Department of Plant Sciences, University of Cambridge, Cambridge, UK; Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
riboSeqR funding source(s)
Supported by an EMBL long-term postdoctoral fellowship, Sir Henry Wellcome Fellowships, a Wellcome Trust PhD scholarship, a Wellcome Trust Fellowship (088789), UK Biotechnology and Biological Sciences Research Council grants. (BB/L000334/1) and (BB/J007072/1).

riboSeqR reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review riboSeqR