Literature DB >> 25812744

RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis.

Rachel Legendre1, Agnès Baudin-Baillieu1, Isabelle Hatin1, Olivier Namy1.   

Abstract

MOTIVATION: Ribosome profiling provides genome-wide information about translational regulation. However, there is currently no standard tool for the qualitative analysis of Ribo-seq data. We present here RiboTools, a Galaxy toolbox for the analysis of ribosome profiling (Ribo-seq) data. It can be used to detect translational ambiguities, stop codon readthrough events and codon occupancy. It provides a large number of plots for the visualisation of these events.
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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Year:  2015        PMID： 25812744     DOI： 10.1093/bioinformatics/btv174

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  23 in total

1.  uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast.

Authors:  Pieter Spealman; Armaghan Naik; Joel McManus
Journal:  Methods Mol Biol       Date:  2021

2.  Detecting actively translated open reading frames in ribosome profiling data.

Authors:  Lorenzo Calviello; Neelanjan Mukherjee; Emanuel Wyler; Henrik Zauber; Antje Hirsekorn; Matthias Selbach; Markus Landthaler; Benedikt Obermayer; Uwe Ohler
Journal:  Nat Methods       Date:  2015-12-14       Impact factor: 28.547

3.  RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.

Authors:  Keren Li; C Matthew Hope; Xiaozhong A Wang; Ji-Ping Wang
Journal:  Nucleic Acids Res       Date:  2020-12-02       Impact factor: 16.971

4.  RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data.

Authors:  Carine Legrand; Francesca Tuorto
Journal:  Nucleic Acids Res       Date:  2020-01-24       Impact factor: 16.971

5.  Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.

Authors:  Joshua G Dunn; Jonathan S Weissman
Journal:  BMC Genomics       Date:  2016-11-22       Impact factor: 3.969

6.  ORFik: a comprehensive R toolkit for the analysis of translation.

Authors:  Håkon Tjeldnes; Kornel Labun; Yamila Torres Cleuren; Katarzyna Chyżyńska; Michał Świrski; Eivind Valen
Journal:  BMC Bioinformatics       Date:  2021-06-19       Impact factor: 3.169

7.  The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

Authors:  Betty Y Chung; Thomas J Hardcastle; Joshua D Jones; Nerea Irigoyen; Andrew E Firth; David C Baulcombe; Ian Brierley
Journal:  RNA       Date:  2015-08-18       Impact factor: 4.942

8.  RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

Authors:  Audrey M Michel; James P A Mullan; Vimalkumar Velayudhan; Patrick B F O'Connor; Claire A Donohue; Pavel V Baranov
Journal:  RNA Biol       Date:  2016-01-29       Impact factor: 4.652

9.  RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.

Authors:  Alexandra Popa; Kevin Lebrigand; Agnes Paquet; Nicolas Nottet; Karine Robbe-Sermesant; Rainer Waldmann; Pascal Barbry
Journal:  F1000Res       Date:  2016-06-09

10.  Global translational impacts of the loss of the tRNA modification t6A in yeast.

Authors:  Patrick C Thiaville; Rachel Legendre; Diego Rojas-Benítez; Agnès Baudin-Baillieu; Isabelle Hatin; Guilhem Chalancon; Alvaro Glavic; Olivier Namy; Valérie de Crécy-Lagard
Journal:  Microb Cell       Date:  2016-01-01
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