Ribosome profiling data analysis bioinformatics software tools
Genome-wide analyses of gene expression have so far focused on the abundance of mRNA species as measured either by microarray or, more recently, by RNA sequencing. However, neither approach provides information on protein synthesis, which is the true end point of gene…
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RiboTaper
Desktop

RiboTaper

A rigorous statistical approach that identifies translated regions on the basis…

A rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from…

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altORFev
Web
Desktop

altORFev altORF evaluator

Predicts alternative open reading frames within eukaryotic mRNA translated by a…

Predicts alternative open reading frames within eukaryotic mRNA translated by a conventional linear scanning mechanism and its modifications (leaky scanning, reinitiation). altORFev reveals…

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RiboDiff
Desktop

RiboDiff

Detects the protein translational efficiency change from Ribo-Seq (ribosome…

Detects the protein translational efficiency change from Ribo-Seq (ribosome footprinting) and RNA-Seq data. RiboDiff uses a generalized linear model to detect genes showing difference in…

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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique…

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Ribosome…
Desktop

Ribosome profiling analysis framework

A dedicated pipeline to identify translation initiation sites (TISs). Ribosome…

A dedicated pipeline to identify translation initiation sites (TISs). Ribosome profiling analysis framework features alignment, triplet periodicity analysis, detecting translation initiation sites…

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PROTEOFORMER
Virtual
Web

PROTEOFORMER

A proteogenomic pipeline that delineates true in vivo proteoforms and generates…

A proteogenomic pipeline that delineates true in vivo proteoforms and generates a protein sequence search space for peptide to MS/MS matching. PROTEOFORMER can be combined with canonical protein…

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riboShape
Desktop

riboShape

Predicts ribosome footprint profile shapes from transcript sequences. Riboshape…

Predicts ribosome footprint profile shapes from transcript sequences. Riboshape is a suite of algorithms. It applies kernel smoothing to codon sequences to build predictive features, and uses these…

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RiboProfiling
Desktop

RiboProfiling

Offers a collection of tools for Ribo-seq data analysis. RiboProfiling provides…

Offers a collection of tools for Ribo-seq data analysis. RiboProfiling provides a unique, straightforward R implementation of a ribosome profiling pipeline from BAM, to P-site calibration,…

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RiboGalaxy
Web

RiboGalaxy

A freely available Galaxy-based web server for processing and analysing…

A freely available Galaxy-based web server for processing and analysing ribosome profiling data with the visualization functionality provided by GWIPS-viz. RiboGalaxy offers researchers a suite of…

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Riborex
Desktop

Riborex

Maps genome-wide differences in translation efficiency. Riborex directly…

Maps genome-wide differences in translation efficiency. Riborex directly leverages established RNA-seq analysis frameworks for all parameter estimation, providing users with a choice among robust…

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riboviz
Web
Desktop

riboviz

Allows convenient exploration and analysis of riboseq datasets. riboviz…

Allows convenient exploration and analysis of riboseq datasets. riboviz consists of a comprehensive and flexible backend analysis pipeline that allows the user to analyze their private unpublished…

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RiboTools
Web

RiboTools

A Galaxy toolbox for the analysis of ribosome profiling (Ribo-seq) data. It can…

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…

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RUST
Web
Desktop

RUST Ribo-Seq Unit Step Transformation

Identifies mRNA sequence features that affect ribosome footprint densities…

Identifies mRNA sequence features that affect ribosome footprint densities globally. RUST is designed for ribo-seq data and produces a metafootprint profile that reveals the influence of mRNA…

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riboSeqR
Desktop

riboSeqR

An R package for the analysis of sequencing data from ribosome profiling…

An R package for the analysis of sequencing data from ribosome profiling experiments. Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

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SPECtre
Desktop

SPECtre

A spectral coherence-based classification algorithm to identify regions of…

A spectral coherence-based classification algorithm to identify regions of active translation using aligned ribosome profiling sequence reads. SPECtre leverages a key feature of ribosome profiling…

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