RiboSeq.Org is a collection of tools and processed datasets that enable users to explore Ribo-Seq and ancillary datasets in the browser
GWIPS-viz is an online genome browser tailored for exploring ribosome profiling (Ribo-seq) data. Since its inception in 2014, GWIPS-viz has evolved significantly and now provides Ribo-seq data for 23 different genomes. It offers a wealth of Ribo-seq tracks, totaling 1792, with a particular emphasis on human-derived data. User-requested features, such as the option to download data in bigWig format, have been incorporated. The platform also includes various types of data, such as TCP-seq, and auxiliary tracks from different sources to aid in interpreting Ribo-seq data. Enhanced visualization techniques have been implemented, especially for bacterial genomes, where Ribo-seq data is displayed in a strand-specific manner. Additionally, GWIPS-viz offers global aggregate tracks, created by aggregating Ribo-seq data from multiple studies, to enhance the signal strength and utility of the platform. It is available at gwips.ucc.ie.
RiboCrypt is a versatile web-based tool designed for in-depth analysis of ribosome profiling (ribo-seq) data and its variants. It offers a rich collection of pre-processed datasets from over 10,000 experiments across 70+ organisms and various experimental conditions. RiboCrypt goes beyond mere data summarization, providing connected modules to explore data at multiple levels of abstraction and in the context of genomic, transcriptomic, and proteomic features. This tool serves as a powerful resource for generating hypotheses and discovering novel instances of translational regulation in a high-throughput manner. Additionally, for power users, RiboCrypt offers a Bioconductor package that enables exploration of various large-scale Next-Generation Sequencing (NGS) data types, enhancing its utility in NGS research. It is available at ribocrypt.org
Trips-Viz is an interactive platform designed for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-Seq) data. It functions as both a database of processed data and an analysis server, providing access to a growing repository of processed Ribo-Seq and RNA-Seq data aligned to reference transcriptomes. Trips-Viz offers a user-friendly interface for exploring and analyzing these datasets, making it a valuable resource for researchers carrying out genomics and proteomics studies. Additionally, it supports the visualization of proteomics data and allows users to upload custom reference transcriptomes and various data types, expanding its versatility and utility in diverse research applications. It is available at trips.ucc.ie.
RiboGalaxy is a Galaxy instance that has been populated with tools for the analysis of ribosome profiling data in the browser. RiboGalaxy has been designed with an emphasis on preparing users datasets for upload to other RiboSeq.Org resources, however, each dataset is easily exported for downstream analysis elsewhere. It is available at ribogalaxy.genomicsdatascience.ie .
Ribo-Seq Data Portal
The Ribo-Seq Data Portal is a web portal that enables users to query and explore existing ribosome profiling and ancillary datasets. The metadata curation and data pre-processing that was carried out during the development of this resource makes large-scale re-analysis of Ribo-Seq data considerably more feasible. It is available at recode.ucc.ie/home.
Other tools produced by members of the RiboSeq.Org team and related researchers include:
Description: ORFik is a comprehensive R package for the analysis of translation
Code Link: github.com/Roleren/ORFik
Publication Link: 10.1186/s12859-021-04254-w
RUST - Ribo-seq Unit Seq Transform
Description: A simple normalization method to limit the impact of the heterogeneity of Ribo-Seq data
Code Link: github.com/JackCurragh/RUST
Publication Link: 10.1038/ncomms1291
Description: Metric based quality assessment for Ribo-Seq data
Code Link: github.com/JackCurragh/RiboMetric
Publication Link: None
Publications that describe RiboSeq.Org resources include:
RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update. (2023) Alla D Fedorova, Jack A S Tierney, Audrey M Michel, Pavel V Baranov J Mol Biol., DOI: 10.1016/j.jmb.2023.168043
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data (2021) Stephen J Kiniry, Ciara E Judge, Audrey M Michel, Pavel V Baranov Nucleic Acids Res., DOI: 10.1093/nar/gkab323
Trips-Viz: a transcriptome browser for exploring Ribo-Seq data. (2019) Stephen J Kiniry, Patrick B F O'Connor, Audrey M Michel, Pavel V Baranov Nucleic Acids Res., DOI: 10.1093/nar/gky842
The GWIPS-viz Browser (2018) Stephen J Kiniry, Audrey M Michel, Pavel V Baranov Curr Protoc Bioinformatics., DOI: 10.1002/cpbi.50
GWIPS-viz: 2018 update. (2018) Audrey M Michel, Stephen J Kiniry, Patrick B F O'Connor, James P Mullan, Pavel V Baranov. Nucleic Acids Res., DOI: 10.1093/nar/gkx790
RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data. (2016) Audrey M Michel, James P A Mullan, Vimalkumar Velayudhan, Patrick B F O'Connor, Claire A Donohue, Pavel V Baranov RNA Biol, DOI: 10.1080/15476286.2016.1141862
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms. (2015) Audrey M Michel, Anna M Ahern, Claire A Donohue, Pavel V Baranov Proteomics, DOI: 10.1002/pmic.201400603
GWIPS-viz: development of a ribo-seq genome browser. (2014) Audrey M Michel, Gearoid Fox, Anmol M Kiran, Christof De Bo, Patrick B F O'Connor, Stephen M Heaphy, James P A Mullan, Claire A Donohue, Desmond G Higgins, Pavel V Baranov Nucleic Acids Res., DOI: 10.1093/nar/gkt1035
Examples of Publications that make use of RiboSeq.Org resources include:
Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5'UTRs. (2023) Author(s) Alexandra Filatova, Ivan Reveguk, Maria Piatkova, Daria Bessonova, Olga Kuziakova, Victoria Demakova, Alexander Romanishin, Veniamin Fishman, Yerzhan Imanmalik, Nikolay Chekanov, Rostislav Skitchenko, Yury Barbitoff, Olga Kardymon, Mikhail Skoblov. Nucleic Acids Res., DOI: 10.1093/nar/gkac1247
Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers. (2021) Author(s) Oza Zaheed, Stephen J Kiniry, Pavel V Baranov, Kellie Dean Front Cell Dev Biol., DOI: 10.3389/fcell.2021.703374
A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset. (2020) Oza Zaheed, Julia Samson, Kellie Dean Noncoding RNA Res., DOI: 10.1016/j.ncrna.2020.02.004