Active ORF detection
PRICE (Probabilistic inference of codon activities by an EM algorithm) is a method to identify ORFs using Ribo-seq experiments embedded in a pipeline for data analysis
RibORF is a computational pipeline to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons.
ORF-RATER (Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.
Ribosome profiling with Bayesian predictions (Rp-Bp) is an unsupervised Bayesian approach to predict translated open reading frames (ORFs) from ribosome profiles, using an automatic Bayesian Periodic fragment length and ribosome P-site offset Selection (BPPS).
RiboCode is a very simple but high-quality computational algorithm to identify genome-wide translated ORFs using ribosome-profiling data.
RiboWave analyses Ribosome profiling data (Ribo-seq). It utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes (i.e. signal frequency) and precisely locate their footprint.
SPECtre is a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
PreTIS is a Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
ORFik is a tool for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges.
Ribo TIS Hunter (Ribo-TISH) is used for identifying translation activities using ribosome profiling data. Ribo-TISH uses statistical tests to assess the significance of translation activities. It captures significant TISs using negative binomial test, and frame biased open reading frames (ORFs) using rank sum test. Ribo-TISH can also perform differential analysis between two TI-Seq data.
Proteoformer is a proteogenomic pipeline that delineates true in vivo proteoforms and generates a protein sequence search space for peptide to MS/MS matching. It can be combined with canonical protein databases or used independently for identification of novel translation products. The pipeline makes use of the recently developed next generation sequencing strategy termed ribosome profiling (Ribo-seq) that provides genome-wide information on protein synthesis in vivo.
ribotricer is a method for detecting actively-translating ORFs by directly leveraging the three-nucleotide periodicity of Ribo-seq data. Ribotricer demonstrates higher accuracy and robustness compared with other methods at detecting actively-translating ORFs including short ORFs on multiple published datasets across species inclusive of Arabidopsis, C. elegans, Drosophila, human, mouse, rat, yeast, and zebrafish.
Translation efficiencies and differential translation analysis
Xtail is an analysis pipeline tailored for ribosome profiling data that comprehensively and accurately identifies differentially translated genes in pairwise comparisons.
Riborex is a computational tool for mapping genome-wide differences in translation efficiency. Riborex shares a similar mathematical structure with existing methods, but has a simplified implementation.
RiboDiff is a statistical tool that detects the protein translational efficiency change from Ribo-seq (ribosome footprinting) and RNA-Seq data. It uses a generalized linear model to detect genes showing difference in translational profile taking mRNA abundance into account. It facilitates us to decipher the translational regulation that behave independently with transcriptional regulation.
Babel is a tool for detecting translation changes from paired mRNA and ribosome protected fragment count data.Babel is based on an errors-in-variables regression model that uses the negative binomial distribution and draws inference using a parametric bootstrap approach.
Anota (analysis of translational activity) is a R-package which implements APV, allows scrutiny of associated statistical assumptions and provides biologically motivated filters for analysis of genome wide datasets. The package can be used for analysis of differential translation in polysome microarray or ribosome-profiling datasets.
Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data. Ribomap addresses this problem by assigning reads to potential origins in the transcriptome proportional to the estimated transcript abundance. This results in a more accurate estimation of the ribosome pileup compared to naive read assignments.
Scikit-ribo is an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data.
Visualization and codon related statistics
RiboProfiling is a Bioconductor package that provides multiple types of Ribo-seq data analysis, starting from BAM files alone:1) Quality assessment of read match size distribution,2) Read coverage around the TSS for the definition of an offset (shift value) of ribosome position,3) Calibrate reads by applying an offset to the read start positions along the transcript,4) Table of read start counts (shifted if specified) on the specified region (CDS, 5pUTR, 3pUTR),5) A graphical quality function for Ribo-seq data, based on the previously obtained tables, 6) The quantification of the frequency and coverage matrices for motifs of codons (1, 2 or 3 codons) in ORFs,7) Principal component analysis of codon motif coverage in ribosome-profiling.
riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.
Shoelaces is a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolution. Shoelaces provides both a user-friendly graphical interface for interactive visualisation in a genome browser-like fashion and a command line interface for integration into automated pipelines.
mQC is a tool to easily generate some figures which give a nice overview of the quality of the mapping of ribosome profiling data. More specific, it gives an overview of the P site offset calculation, the gene distribution and the metagenic classification. Furthermore, MappingQC does a thorough analysis of the triplet periodicity and the linked triplet phase (typical for ribosome profiling) in the canonical transcript of your data.
RiboTools is a Galaxy toolbox for the analysis of ribosome profiling (Ribo-seq) data. It can be used to detect translational ambiguities, stop codon read through events and codon occupancy.
riboSeqR provides a set of methods for parsing ribosomal profiling data from multiple samples, aligning to coding sequences, inferring alternative reading frames, and plotting average and transcript-specific behavior of these data.
The GWIPS-viz browser is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data.
Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays.
XPRESSpipe, a part of the XPRESSyourself suite of sequencing tools, is an automated, efficient, and flexible pipeline for end-to-end processing of ribosome profiling data. XPRESSpipe is currently capable of handling single-end (SE), paired-end (PE), and ribosome profiling data.
PausePred is a tool which can be used to infer ribosome pauses from ribosome profiling (Ribo-seq) data. Peaks of ribosome footprint density are scored based on their magnitude relative to the background density within the surrounding area. The scoring allows the comparison of peaks across the transcriptome or genome.
RiboAbacus is a mathematical model that for the first time incorporates imaging data in a predictive model of transcript-specific ribosome densities and translational efficiencies.
RiboGalaxy is a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz.
Trips-viz is a transcriptome browser designed to visualize Ribosome profiling and RNA-seq data at the level of a single gene/transcript isoform as opposed to at the genome level.
riboviz is a tool-kit for analyzing and visualizing ribosome profiling datasets. RiboViz consists of a comprehensive and flexible backend analysis pipeline and a web application for visualization. The current iteration of *RiboViz is designed for yeast datasets.
systemPipeR is a ribo-seq analysis workflow, including read preprocessing, read alignments against a reference genome, counting of reads overlapping with a wide range of genomic features (e.g. CDSs, UTRs, uORFs, rRNAs, etc.), differential gene expression and differential ribosome binding analyses, ORF calling as well as a variety of genome-wide summary plots for visualizing RNA expression trends.
RiboVIEW is a package of tools to compute and visualize results, perform quality control, and derive an unbiased estimate of codon enrichment. We offer the user a webpage view to scan own data on the following aspects: periodicity, ligation and digestion of ribosome-protected footprints; reproducibility and batch effects of replicates; drugs-related artifacts; codon enrichment including variability observed between mRNAs and positions for ribosome acceptor, peptidyl and exit (A, P and E, respectively) sites; mining of causal or confounding factors.
riboStreamR is a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application. RiboStreamR provides visualization and analysis tools for various Ribo-seq QC metrics, including read length distribution, read periodicity, and translational efficiency.
Ribo Ecosystem is a set of software tools, built around the ribo file format, to facilitate analyzing ribosome profiling data at ribosome protected footprint length resolution. It consists of a pipeline, RiboFlow, and two interfaces RiboR and RiboPy.
Databases
PRFdb (v2.0) is a database which currently hosts 2884 Ribo-seq datasets from 293 studies, covering 29 different species. In line with the significant expansion of Ribo-seq data available in the database, RPFdb v2.0 includes a refined analysis pipeline with multi-step quality control applied for improving the pre-processing and alignment of Ribo-seq data, new functional modules providing actively translated ORFs information, and more web features for better database usability.
TranslatomeDB is a comprehensive database which provides collection and integrated analysis of published and user-generated translatome sequencing data. It includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels.
HRPDviewer, the Human Ribosome Profiling Data viewer, contains 610 published human Ribo-seq datasets from Gene Expression Omnibus, aligns the Ribo-seq data to the transcriptome and provides visualization of the Ribo-seq data on the selected mRNA transcripts.
OpenProt is the first database that enforces a polycistronic model of eukaryotic genome annotations. Thus, OpenProt annotates known proteins (called RefProts) but also novel isoforms and novel proteins (called altProts). It also provides supporting evidence for each protein, such as mass-spectrometry and ribosome profiling detection, protein homology and predictions of functional domains.