Software of Ribo-seq data analysis

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  • Software tools

    • Data preprocessing

    18 tools

    1 tool

    1 tool


    18 tools

    5 tools

    1 tool


    2 tools

    10 tools

    9 tools


    Data preprocessing

    Tool Description Manual Reference
    Plastid A python library that is designed to retain the user-friendly pipeline tools for nucleotide-resolution analysis of NGS data, such as ribo-seq and RNA-seq Dunn JG et al.2016
    PROTEOFORMER2.0 A proteogenomic pipeline for automatically processing ribo-seq data to allow genome-wide visualization of ribosome occupancy and delineating in vivo proteoforms to build an optimal protein sequence search database for peptide to Mass spectrometry/mass spectrometry (MS/MS) matching Steven Verbruggen, 2019
    ribodeblur A python package for estimating the ribosome A-site position signals from ribo-seq data Wang H et al.2017
    RiboPlot A python package that provides riboplot and ribocount programs to plot and output read counts of ribo-seq data Michel AM et al.2016
    RiboProfiling An R/Bioconductor package that provides a full pipeline to cover all key steps for facilitating quality assessment and quantification of ribo-seq experiments Popa A et al.2016
    RiboTools A Galaxy toolbox for the analysis of ribo-seq data that is dedicated to detecting translational ambiguities, stop codon readthrough events and codon occupancy of ribosomal A, P and E-sites - Legendre R et al.2015
    riboraptor A pipeline for analysing ribosome profiling data -
    PausePred and Rfeet Webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data Romika Kumari et al.2018
    RSCU Measuring the bias in codon usage from ribosomal activity Damien Paulet et al.2017
    Start - Stop codon analysis Workflow for start, stop codon analysis for Ribosome Protected Fragments -
    mQC A tool to easily generate some figures which give a nice overview of the quality of the mapping of ribosome profiling data Steven Verbruggen et al.2018
    riboWaltz Optimization of ribosome P-site positioning in ribosome profiling data Fabio Lauria et al.2018
    RIVET RIVET is a simple to use R-shiny based graphical user interface to automate the statistical analysis of RNA sequencing data and microarray data generated by either polysome profiling or ribosome footprinting Amanda W. Ernlund et al.2018
    XPRESSpipe XPRESSpipe is an automated, efficient, and flexible pipeline for processing RNA-seq raw data, performing quality control analysis on the data, and preparing data for further downstream analysis Jordan A. Berg et al.2019
    RiboPip A Ruby-based alignment and analysis pipeline for Ribo-seq and RNA-seq data -
    riboSeqR An R/Bioconductor package that provides a set of programs for processing, analyzing and displaying ribo-seq data Chung BY et al.2015
    ribosome-profiling-analysis-framework A dedicated pipeline for identifying TISs de Klerk E et al.2015
    systemPipeR An R/Bioconductor package for building and running automated end-to-end analysis workflows for a wide range of NGS applications, including ribo-seq Backman TWH et al.2016

    RNase footprint examination

    Tool Description Manual Reference
    Rfoot A computational pipeline for identifying RNA regions protected by nonribosomal RNA–protein complexes Ji Z et al.2016

    Data normalization

    Tool Description Manual Reference
    RUST A smoothing transformation-based approach for ribo-seq normalization O’Connor PB et al.2016

    Isoform-level footprint

    Tool Description Manual Reference
    Ribomap An isoform-level ribosome occupancy estimation approach for quantifying isoform-level ribosome profiles Wang H et al.2016
    riboshape A sparse regression model for predicting ribosome footprint profile shapes from transcript sequences Liu TY et al.2016

    Translation or synthesis rate inference

    Tool Description Manual Reference
    Absolute Synthesis Rates for measuring absolute protein synthesis rates -
    Pop A flow conservation-based model for extracting codon translation rates and protein synthesis rates - Pop C et al.2014
    SMoPT A continuous-time, discrete-state Markov model for studying the dynamics of protein translation Shah P et al.2013
    TASEP A totally asymmetric simple exclusion process-based approach for inferring translation kinetics
    RFMapp enabling the estimation of the translation elongation rates of messenger ribonucleic acids (mRNAs) and the profile of ribosomal densities along the mRNAs Hadas Zur et al.2012

    Ribosome stalling event prediction

    Tool Description Manual Reference
    ROSE A deep learning-based framework for predicting ribosome stalling events Sai Zhang et al.2017

    ORF discovery and annotation

    Tool Description Manual Reference
    RibORF A support vector machine-based classifier for identifying actively translated ORFs Zhe Ji et al.2018
    RiboTaper A multitaper spectral-based approach for detecting actively translated ORFs Lorenzo Calviello et al.2015
    RiboCode De novo annotation and characterization of the translatome with ribosome profiling data Zhengtao Xiao et al.2018
    ribotricer Accurate detection of short and long active ORFs using Ribo-seq data Saket Choudhary et al.2020
    ribotish Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data Peng Zhang et al.2017
    ribowave RiboWave is a funtional Ribo-seq analysis tool to identify translated ORF based on Ribo-seq data. Zhiyu Xu et al.2018
    AltORFev the prediction of alternative open reading frames in eukaryotic mRNAs Alex V Kochetov et al.2017
    uORF-Tools uORF-Tools are a workflow and a collection of tools for the analysis of 'upstream Open Reading Frames' Scholz A et al.2019
    PRICE A method to identify open reading frames (ORF) using Ribosome profiling (Ribo-seq) experiments embedded in a pipeline for data analysis Florian Erhard et al.2018
    FLOSS A fragment length organization similarity metric for classifying the translation status of individual transcripts and subregions - Ingolia NT et al.2014
    ORF-RATER A regression-based approach for annotating protein-coding sequences Fields AP et al.2015
    ORFscore A metric for exploring high-resolution footprinting with ribosome phasing to identify actively translated sORFs Bazzini AA et al.2014
    PTS A periodicity transition metric for detecting dual-coding regions by spotting frame preference changes - Michel AM et al.2012
    riboHMM A mixed hidden Markov model-based approach for inferring translated sequences Raj A et al.2016
    Rp-Bp An unsupervised Bayesian approach for predicting translated ORFs Malone B et al.2017
    RRS A metric for measuring ribosome release at bona fide stop codons to detect translation through ORFs Guttman M et al.2013
    SPECtre A spectral coherence-based classifier for identifying regions of active translation Chun SY et al.2016
    TOC A random forest classifier for distinguishing ORFs in annotated 50 leaders, coding sequences (CDSs) and 30 trailers - Chew GL et al.2016

    Differential translation

    Tool Description Manual Reference
    RiboDiPA RiboDiPA allows for quick identification of genes with statistically significant differences in ribosome occupancy patterns for model organisms ranging from yeast to mammals. Wang et al. 2020
    RiboDiff A generalized linear model-based framework for detecting genes with changes in translation efficiency across experimental conditions Zhong Y et al.2017
    anota An R/Bioconductor package for applying per-gene analysis of partial variance coupled with variance shrinkage to identify differential translation Larsson O et al.2011
    Babel An errors-in-variables regression model-based framework for inferring genes with changes in translational regulation within cells and between conditions Olshen AB et al.2013
    diricore A procedure for differential ribosome measurements of codon reading Loayza-Puch F et al.2016
    Riborex A generalized linear model-based tool for identifying genes exhibiting differential translation Li W et al.2017
    tRanslatome A complete platform for the analysis of differential profiles coming from transcriptome, translatome and proteome studies Tebaldi T et al.2014
    Xtail An analysis pipeline tailored for ribo-seq data to quantify the magnitudes and statistical significances of differential translations at the genome-wide scale Xiao Z et al.2016
    anota2seq It provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Christian Oertlin et al.2019
    ribofootprintR Fast data processing for ribosome footpring profiling experiments from bam files -

    Analysis and visualization

    Tool Description Manual Reference
    RiboMiner RiboMiner performs extensive quality assessment of the data and integrates a spectrum of tools for various metagene analyses of the ribosome footprints and for detailed analyses of multiple features related to translation regulation. Yang et al. 2020
    RiboToolkit A convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. Gregory et al. 2020
    RiboFlow, RiboR and RiboPy Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots and carry out analyses. Cenik et al. 2020
    XPRESSyourself Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data. Rutter et al. 2020
    RiboVIEW a computational framework for visualization, quality control and statistical analysis of ribosome profiling data Carine Legrand, Francesca Tuorto 2019
    riboviz analysis and visualization of ribosome profiling datasets Oana Carja et al.2017
    Shoelaces An interactive tool for ribosome profiling processing and visualization Åsmund Birkeland et al.2018
    RiboseqTools Tools for ribosome profiling data analysis and plot -
    XPRESSplot XPRESSplot is a Python toolkit for navigating and analyzing gene expression (Microarray or RNAseq) datasets Jordan A. Berg et al.2019