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https://github.com/JackCurragh/awesome-riboseq
A list of bioinformatic tools for working with Ribo-Seq data
https://github.com/JackCurragh/awesome-riboseq
List: awesome-riboseq
Last synced: 3 months ago
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A list of bioinformatic tools for working with Ribo-Seq data
- Host: GitHub
- URL: https://github.com/JackCurragh/awesome-riboseq
- Owner: JackCurragh
- License: mit
- Created: 2023-01-10T13:12:28.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-04-11T17:38:04.000Z (7 months ago)
- Last Synced: 2024-04-11T22:16:45.045Z (7 months ago)
- Size: 67.4 KB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Awesome Ribo-Seq
A list of bioinformatic tools for working with Ribo-Seq data. Please feel free to make updates
(a work in progress)
## Table of Contents
## Table of Contents
- [Data Resources and Visualisation Environments](#data-resources-and-visualisation-environments)
- [Data Processing and Analysis](#data-processing-and-analysis)
- [Differential Analysis](#differential-analysis)
- [Quality Control](#quality-control)
- [Offset Determination](#offset-determination)
- [ORF Calling](#orf-calling)
- [ORF Databases](#orf-databases)
- [Isoform Level Analysis](#isoform-level-analysis)
- [Ribo-Seq Simulation](#ribo-seq-simulation)
- [Occupancy Analysis](#occupancy-analysis)
- [Pause Prediction](#pause-prediction)
- [Frameshift Detection](#frameshift-detection)
- [Misc](#misc)
## Data Resources and Visualisation Environments
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| Trips-Viz | [Code](https://github.com/riboseqorg/Trips-Viz) | [Reference](https://doi.org/10.1093/nar/gkab323) | Written in Python; Browser only; [Link](https://trips.ucc.ie); Transcriptome |
| GWIPS-viz | [Code](https://github.com/riboseqorg/GWIPS-viz) | [Reference](https://doi.org/10.1093/nar/gkt1035) | Based on UCSC Genome Browser; Browser only; [Link](https://gwips.ucc.ie); Genome |
| RiboCrypt | [Code](https://github.com/m-swirski/RiboCrypt) | [Reference]() | Written in R; Available in Bioc; Genome aligned; Visualisation in both |
| RPFdb | [Code]() | [Reference](https://doi.org/10.1093/nar/gky978) | Browser only; Counts and Called ORFs (RibORF) available per study; Genome; [Link](http://sysbio.gzzoc.com/rpfdb/) |
| HRPDviewer | [Code](http://cosbi4.ee.ncku.edu.tw/HRPDviewer/user/help_p1#collect2) | [Reference](https://doi.org/10.1093/database/bay074) | Pipeline available in .zip only' Written in Python; Transcriptome |
| HRPDviewer | [Code](http://cosbi4.ee.ncku.edu.tw/HRPDviewer/user/help_p1#collect2) | [Reference](https://doi.org/10.1093/database/bay074) | Pipeline available in .zip only' Written in Python; Transcriptome |
| RiboSeqDB | [Code]() | [Reference](https://doi.org/10.12704/vb/e18) | Appears to be defunct |
| TranslatomeDB | [Code]() | [Reference](https://doi.org/10.1093/nar/gkx1034) | Transcriptome aligned with FANSe3; [Link](http://translatomedb.net/) |
| svist4get | [Code](https://github.com/art-egorov/svist4get) | [Reference](https://doi.org/10.1186/s12859-019-2706-8) | Command line app; Genomic |
| RiboPlot | [Code](https://github.com/vimalkvn/riboplot) | [Reference]() | Python; Archived |
| RiboPlotR | [Code](https://github.com/hsinyenwu/RiboPlotR) | [Reference](https://doi.org/10.1186/s13007-021-00824-4) | R; Similar transcript plotting to RiboCrypt (w/ multiple isoforms)|
| RiboGraph | [Code](https://github.com/ribosomeprofiling/ribograph) | [Reference](https://doi.org/10.1101%2F2024.01.11.575228)| Docker image; Endpoint for RiboPy |
## Data Processing and Analysis
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| riboviz | [Code](https://github.com/riboviz/RiboViz) | [Reference](https://doi.org/10.1093/bioinformatics/btac093) | Nextflow (DSL1); End-to-end processing and analysis |
| Shoelaces | [Code](https://bitbucket.org/valenlab/shoelaces/src/master/) | [Reference](https://doi.org/10.1186/s12864-018-4912-6) | Written in python |
| ORFik | [Code](https://github.com/Roleren/ORFik) | [Reference](https://doi.org/10.1186/s12859-021-04254-w ) | Written in R; Available on Bioc; End-to-end |
| RiboProfiling | [Code](https://bioconductor.org/packages/release/bioc/html/RiboProfiling.html) | [Reference](https://doi.org/10.12688/f1000research.8964.1) | Written in R; Available on Bioc; Analysis Package |
| SystemPipeR | [Code](https://bioconductor.org/packages/release/bioc/html/systemPipeR.html) | [Reference](https://doi.org/10.1186/s12859-016-1241-0) | Written in R; Available on Bioc; End-to-end |
| RiboStreamR | [Code](https://github.com/pjperki2/riboStreamR) | [Reference](https://doi.org/10.1186/s12864-019-5700-7) | Written in R; Available as web app |
| RiboSeqR | [Code](https://bioconductor.org/packages/release/bioc/html/riboSeqR.html) | None | Written in R; Available in Bioc; Analysis and visualisation |
| RiboPip | [Code](https://github.com/stepf/RiboPip) | None | Written in Ruby; Comes with Dockfile; End-to-end |
| RiboGalaxy | [Code](https://github.com/riboseqorg/RiboGalaxy) | [Reference](https://doi.org/10.1080/15476286.2016.1141862) | Galaxy Platform; Tools in toolshed; Data Processing; [Link](https://ribogalaxy.genomicsdatascience.ie/) |
| Plastid | [Code](https://github.com/joshuagryphon/plastid) | [Reference](https://doi.org/10.1186/s12864-016-3278-x) | Written in Python; Packaged on PyPi; Analysis |
| RiboTools | [Code]() | [Reference](https://doi.org/10.1093/bioinformatics/btv174) | Galaxy Platform; Tools in toolshed; Analysis |
| RiboFlow, RiboR and RiboPy | [Code](https://github.com/ribosomeprofiling) | [Reference](https://doi.org/10.1093/bioinformatics/btaa028) | Ecosystem of tools; Nextflow (DSL1), R and Python; End-to-end |
| RiboToolKit | [Code]() | [Reference](https://doi.org/10.1093/nar/gkaa395) | Browser only; End-to-end; [Link](http://rnainformatics.org.cn/RiboToolkit/) |
| XPRESSpipe | [Code](https://github.com/XPRESSyourself/XPRESSpipe/tree/main/xpresspipe) | [Reference](https://doi.org/10.1371/journal.pcbi.1007625) | Written in Python, R & C++; End-to-end |
| Ohler-Lab Pipeline | [Code](https://github.com/ohlerlab/Riboseq_Pipeline) | None | Not a published pipeline; R; Shell; ORFquant; RiboseQC |
| Bushell-Lab Pipeline | [Code](https://github.com/Bushell-lab/Ribo-seq) | None | Not a published pipeline; R; Shell; End-to-end |
| Saket Choudhary Pipeline | [Code](https://github.com/saketkc/ribo-seq-snakemake) | None | Not a published pipeline; Snakemake; STAR; RSEM |
| Firth Lab Ribo-Seq Manual | [Code](https://github.com/AndrewFirth12/RiboseqAnalysis) | None | Not a published pipeline; Tutorial; Shell |
| USA FDA Ribo-Seq Pipeline | [Code](https://github.com/FDA/Ribosome-Profiling) | None | Not a published pipeline; Python; HISAT |
| scRibo-Seq paper | [Code](https://github.com/mvanins/scRiboSeq_manuscript) | [Reference](https://doi.org/10.1038/s41586-021-03887-4) | Publication Code; Nextflow; R for figures |
| STATR | [Code](https://github.com/robinald/STATR) | [Reference](https://doi.org/10.1007/s12275-020-9536-2) | Bacterial Ribo-Seq pipeline; Shell; Python; R |
| Ribomake | [Code](https://github.com/nzhang89/Ribomake) | [Reference]() | Ribo-Seq Data Processing; Snakemake; Paired with RiboSeeker |
| RiboSeeker | [Code](https://github.com/nzhang89/RiboSeeker) | [Reference]() | Downstream Analysis; R; Paired with Ribomake |
| Riboconsensus | [Code](https://github.com/pechmannlab/riboconsensus) | [Reference](https://doi.org/10.1111/febs.15748) | Python; Translation Heterogeneity |
| RiboDoc | [Code](https://github.com/equipeGST/RiboDoc) | [Reference](https://doi.org/10.1016/j.csbj.2021.05.014) | Docker; R; Image for end-to-end ribo-seq analysis |
| RiboLog | [Code](https://github.com/goodarzilab/Ribolog) | [Reference](https://doi.org/10.1038/s41556-023-01141-9) | R; Regression based tools for Ribo-Seq analysis Heterogeneity |
| RiboFootprintR | [Code](https://github.com/celalp/ribofootprintR) | [Reference]() | R; Pipeline for data processing |
| RibofootPrinter | [Code](https://github.com/guydoshlab/ribofootPrinter) | [Reference](https://doi.org/10.1101/2021.07.04.451082) | Python; Toolbox for data analysis; |
| MassiveNGSPipe | [Code](https://github.com/rc-biotech/massiveNGSpipe) | [Reference]() | R; Fully automated end to end data processing; RiboCrypt data processing |
| mRibo | [Code](https://github.com/dgelsin/mRibo) | [Reference](https://doi.org/10.1093/nar/gkaa304) | Python; meta-gene analysis on microbial (Bacteria and Archaea) data |
## Differential Analysis
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| Anota2Seq | [Code](https://bioconductor.org/packages/release/bioc/html/anota2seq.html) | [Reference](https://doi.org/10.1093/nar/gkz223) | Written in R; Avaialble in Bioc |
| Babel | [Code](https://cran.r-project.org/web/packages/babel/index.html) | [Reference](https://doi.org/10.1093/bioinformatics/btt533) | Written in R; Available in CRAN; EdgeR |
| RiboDiff | [Code](https://github.com/ratschlab/RiboDiff) | [Reference](https://doi.org/10.1093/bioinformatics/btw585) | Python2, Galaxy, [Link](https://galaxy.inf.ethz.ch/?tool_id=ribodiff), GLM |
| Riborex | [Code](https://github.com/smithlabcode/riborex) | [Reference](https://doi.org/10.1093/bioinformatics/btx047) | Written in R; Conda installation; DEseq2, EdgeR, Voom; |
| RIVET | [Code](https://github.com/ruggleslab/rivet) | [Reference](https://doi.org/10.1186/s12864-018-5166-z) | Written in R; R Shiny app; Link defunct; EdgeR/Limma |
| Xtail | [Code](https://github.com/xryanglab/xtail) | [Reference](https://doi.org/10.1038/ncomms11194) | Written in R; Available in DockerHub; Probability Distribution based |
| RiboDiPa | [Code](https://github.com/jipingw/RiboDiPA) | [Reference](https://doi.org/10.1093/nar/gkaa1049) | Written in R; Available in Bioc; Differential analysis of binned p-seq counts |
| DeltaTE | [Code](https://github.com/SGDDNB/translational_regulation) | [Reference](https://doi.org/10.1002/cpmb.108) | Written in R; Differential analysis; DESeq2 |
## Quality Control
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| MQc | [Code](https://github.com/Biobix/mQC) | [Reference](https://doi.org/10.1016/j.cmpb.2018.10.018) | Written in Perl, Python 2, R; Available on Galaxy and Conda |
| Ribo-seQC | [Code](https://github.com/ohlerlab/RiboseQC) | [Reference](https://doi.org/10.1101/601468) | Written in R |
| RiboQC | [Code](https://github.com/carinelegrand/RiboVIEW) | [Reference](https://doi.org/10.1093/nar/gkz1074) | Written in R; Part of RiboVIEW |
| ribosomeProfilingQC | [Code](https://rdrr.io/bioc/ribosomeProfilingQC/) | [Reference](https://doi.org/10.18129/B9.bioc.ribosomeProfilingQC) | Written in R; Available on Bioc; Reference in Bioc link |
| ORFikQC | [Code](https://github.com/Roleren/ORFik) | [Reference](https://doi.org/10.1186/s12859-021-04254-w) | Written in R; Available on Bioc; Part of ORFik |
| RiboScore | [Code](https://github.com/keanejm/RiboScore) | None | Written in Python; |
Note: Many more tools carry out QC as part of their functionality. Above are those that have individual QC specific modules (that I have seen so far).
## Offset Determination
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| Ribodeblur | [Code](https://github.com/Kingsford-Group/ribodeblur) | [Reference](https://doi.org/10.1089/cmb.2016.0147) | Written in Python |
| RiboProP | [Code](http://bioserv.mps.ohio-state.edu/RiboProP/) | [Reference](https://doi.org/10.1093/bioinformatics/bty854) | Written in Julia; MNase Offset detection |
| RiboWaltz | [Code](https://github.com/LabTranslationalArchitectomics/riboWaltz) | [Reference](https://doi.org/10.1371/journal.pcbi.1006169) | Written in R; Available in Bioconda |
| Integer Programming | [Code](https://github.com/nabeel-bioinfo/Asite_IP_method) | [Reference](https://doi.org/10.1038/s41598-019-42348-x) | Written in Python; Paper contains comparison of methods |
| Scikit-ribo | [Code](https://github.com/hanfang/scikit-ribo) | [Reference](https://doi.org/10.1016/j.cels.2017.12.007) | Written in Python; Also estiamtes translation efficiency |
| RiboA | [Code](https://github.com/obrien-lab/aip_web_docker) | [Reference](https://doi.org/10.1186/s12859-021-04068-w) | Written in Python; Django app in docker image; GUI for Integer Programming method above |
Note: Many many tools carry out offset determinations. These ones advertise it as a main feature.
## ORF Calling
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| DeepRibo | [Code](https://github.com/Biobix/DeepRibo) | [Reference](https://doi.org/10.1093/nar/gkz061) | Python3/PyTorch; Prokaryotes; Ribo-Seq + SD sequence |
| RiboTricer | [Code](https://github.com/smithlabcode/ribotricer) | [Reference](https://doi.org/10.1093/bioinformatics/btz878) | Python; 3' periodicity based |
| orfRater | [Code](https://github.com/alexfields/ORF-RATER) | [Reference](https://doi.org/10.1016/j.molcel.2015.11.013) | Python, Regression based |
| PreTis | None Found | [Reference](https://doi.org/10.1371/journal.pcbi.1005170) | No code available; Webservice; Regression based TIS |
| PRICE | [Code](https://github.com/erhard-lab/price) | [Reference](https://doi.org/10.1038%2Fnmeth.4631) | Available as part of Gedi; Probablistic inference by EM |
| Proteoformer | [Code](https://github.com/Biobix/proteoformer) | [Reference](https://doi.org/10.1074/mcp.RA118.001218) | ORF calling for MS validation; Python, Perl |
| REPARATION | [Code](https://github.com/Biobix/REPARATION) | [Reference](https://doi.org/10.1093/nar/gkx758) | Reannoation of Bacterial Genomes; Perl |
| RiboCode | [Code](https://github.com/xryanglab/RiboCode) | [Reference](https://doi.org/10.1093/nar/gky179) | Wilcoxon Signed rank test of 3 frames; Python; On Bioconda |
| riboHMM | [Code](https://github.com/rajanil/riboHMM) | [Reference](https://doi.org/10.7554/eLife.13328) | Python2; Limits to 1 coding sequence per transcript |
| RibORF | [Code](https://github.com/zhejilab/RibORF) | [Reference](https://doi.org/10.1002/cpmb.67) | Perl; 3' periodicity, uniformness; |
| Ribosome profiling analysis framework | [Code](https://github.com/LUMC/ribosome-profiling-analysis-framework) | [Reference](http://dx.doi.org/10.1093/nar/gkv281) | PHP, Organism must be on [Mutalyzer](https://mutalyzer.nl/) |
| RiboTaper | [Code](https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/) | [Reference](https://doi.org/10.1038/nmeth.3688) | R; Multitaper analysis of triplet; Bioconda, Galaxy; |
| Ribo-TISH | [Code](https://github.com/zhpn1024/ribotish) | [Reference](https://doi.org/10.1038/s41467-017-01981-8) | Python; TI-seq (TIS Hunter); Supports differential initiation analysis |
| RiboWave | [Code](https://github.com/lulab/Ribowave) | [Reference](https://doi.org/10.1093/nar/gky533) | R, Perl, Shell; Wavelet Transform; |
| Rp-Bp | [Code](https://github.com/dieterich-lab/rp-bp) | [Reference](https://doi.org/10.1093/nar/gkw1350) | Python; End-to-end pipeline; Bayesian Periodic fragment length and ribosome P-site offset Selection |
| SPECtre | [Code](https://github.com/mills-lab/spectre) | [Reference](https://doi.org/10.1186%2Fs12859-016-1355-4) | Python; Spectral analysis of sliding windows |
| uORF-seqr | [Code](https://github.com/pspealman/uorfseqr) | [Reference](https://doi.org/10.1101/gr.221507.117) | R; ML-approach; Methods unclear as paper describes regression |
| uORF4u | [Code](https://github.com/GCA-VH-lab/uorf4u) | [Reference](https://doi.org/10.1101/2022.10.27.514069) | Python; Not Ribo-Seq; Conservation based; One 5' UTR at a time |
| ORFLine | [Code](https://github.com/boboppie/ORFLine) | [Reference](https://doi.org/10.1093/bioinformatics/btab339) | Shell, R, Perl, Python; End-to-end; Plastid + ORFscore |
| RiboNT | [Code](https://github.com/songbo446/RiboNT/) | [Reference](https://doi.org/10.3390/life11070701) | Python; Noise tolerence |
| Ribofy | [Code](https://github.com/ncrnalab/ribofy) | None Found | Python; Statistical enrichment on inframe P-sites |
| HRIBO | [Code](https://github.com/RickGelhausen/HRIBO) | [Reference](https://doi.org/10.1093/bioinformatics/btaa959) | Snakemake; Bacterial ORF Detection; DeepRibo; REPARATION |
| uORF_Annotator | [Code](https://github.com/bioinf/uORF_annotator) | [Reference](https://doi.org/10.1093/nar/gkac1247) | Python; Manually annotated training set; ORF and TIS prediction (according to paper) |
| iRibo | [Code](https://github.com/CarvunisLab/iRibo) | [Reference](https://doi.org/10.1016/j.xpro.2023.102826) | C++; Binomial test for three nucleotide; Empirical false discovery rate; Aggregated data periodicity |
| ORFScore | [Code]() | [Reference](https://doi.org/10.1002%2Fembj.201488411) | # in-frame reads; Comparison to uniform dist |
| AltORFev | [Code]() | [Reference](https://doi.org/10.1093/bioinformatics/btw736) | No Code & web app broken - scanning based mechanism of ORF prediction |
## ORF Databases
| Tool | Link | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| sORFs.org | [Link](http://www.sorfs.org/#) | [Reference](https://doi.org/10.1093/nar/gkx1130) | ORFs Detected with Proteoformer; Pride reprocessing |
| OpenProt | [Link](https://openprot.org/p/ng/Home) | [Reference](https://doi.org/10.1093/nar/gkaa1036) | Ribo-Seq + Mass Spec; Polycistronic gene models |
| smProt | [Link](http://bigdata.ibp.ac.cn/SmProt/index.html) | [Reference](https://doi.org/10.1016/j.gpb.2021.09.002) | Small protein database rather than ORFs |
| nORFs.org | [Link](https://norfs.org/home) | [Reference](https://doi.org/10.1038/s41525-020-00167-4) | Aggregated database of OpenProt and sORFs.org; Nice UI |
| uORF-db | [Link](https://www.compgen.uni-muenster.de/tools/uorfdb/index.pl?) | [Reference](https://doi.org/10.1093/nar/gkac899) | "Literature, sequence, and variation data in a central hub" |
| | [Link]() | [Reference]() | |
## Isoform Level Analysis
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| Ribomap | [Code](https://github.com/Kingsford-Group/ribomap) | [Reference](https://doi.org/10.1093/bioinformatics/btw085) | C++; Salmon; Isoform level ribosome profiles based on transcript abundance |
| ORFquant | [Code](https://github.com/lcalviell/ORFquant) | [Reference](https://doi.org/10.1038/s41594-020-0450-4) | R; Isoform level translation quantification of ORFs |
| ORQAS | [Code](https://github.com/comprna/ORQAS) | [Reference](https://doi.org/10.1038/s41467-020-15634-w) | Python, Shell; Isoform level quantification extending Ribomap |
| RPiso | [Code](https://hub.docker.com/r/n26091225/rpiso) | [Reference](https://doi.org/10.1186%2Fs12859-021-04192-7) | Perl; RSEM: Isoform level analysis |
| RiboZINB | [Code](https://github.com/Biobix/RiboZINB) | None Found | Perl, R; Identifying actively translated isoform |
| DeepShape | [Code](https://github.com/cuihf06/DeepShape) | [Reference](https://doi.org/10.1186/s12859-019-3244-0) | Python; RNA-Seq free Isoform level quantification |
| RiboCalc | [Code](https://github.com/gao-lab/RiboCalc) | [Reference](https://doi.org/10.1093/bib/bbab483) | R; quantitatively modeling of coding ability |
| RiboMIMO | [Code](https://github.com/tiantz17/RiboMIMO) | [Reference](https://doi.org/10.1371/journal.pcbi.1008842) | Python; Multi-Input Multi-Output full isoform density prediction |
| | [Code]() | [Reference]() | |
## Ribo-Seq Simulation
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| RiboSimR | [Code]() | [Reference](https://doi.org/10.1007/978) | R; Simulation and Power analysis; [Available](https://pjperki2.shinyapps.io/power/) |
| coverageSim | [Code](https://github.com/Roleren/coverageSim) | [Reference](https://doi.org/10.1007/978) | R; Comprehensive simulation of full profiles |
| simRiboSeq | [Code](https://github.com/lareaulab/simRiboSeq) | [Reference](https://doi.org/10.1101/2023.02.21.529452) | R; Footprint simulator; Unclear differences with coverageSim |
| Ribo-Seq Modelling | [Code](https://github.com/eds35016/5-Ribo-seq-Modeling-Scripts) | [Reference](https://doi.org/10.1101/2023.02.21.529452) | R; Footprint simulator; Unclear differences with coverageSim |
## Occupancy Analysis
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| RUST | [Code](https://github.com/JackCurragh/RUST) | [Reference](https://doi.org/10.1038/ncomms12915) | Python; Unit step transform; Meta analysis |
| Ribo-DT | [Code](https://github.com/cgob/codonDT_snakemake) | [Reference](https://doi.org/10.1016/j.ymeth.2021.10.004) | Snakemake; generalized linear model (GLM) |
| Concur | [Code](https://github.com/susbo/concur) | [Reference](https://doi.org/10.1093/bioinformatics/btaa733) | Perl; R; Codon counts from Ribo-seq |
| Diricore | ["Available On Request"]() | [Reference](https://doi.org/10.1038/nature16982) | |
## Pause Prediction
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| PausePred | [Code](https://github.com/romikasaini/Pausepred_offline) | [Reference](https://doi.org/10.1261/rna.065235.117) | Perl; Sliding Window |
| ROSE | [Code](https://github.com/mlcb-thu/rose) | [Reference](https://doi.org/10.1016/j.cels.2017.08.004) | Python; Scikit-learn |
## Frameshift Detection
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| ORFeus | [Code](https://github.com/morichardson/ORFeus) | [Reference](https://doi.org/10.1186/s12859-023-05602-8) | Python; HMM; detects many different alt-ORF types |
## Misc
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| RFoot | [Code](https://github.com/zhejilab/Rfoot/) | [Reference](https://doi.org/10.1002%2Fcpmb.66) | Perl; Finding RNA-Protein complexes from Ribo-Seq |
| choros | [Code](https://github.com/lareaulab/choros) | [Reference](https://doi.org/10.1101/2023.02.21.529452) | R; Estimate and Correct Sequence Bias in Ribo-Seq |
| RiboReport | [Code](https://github.com/RickGelhausen/RiboReport) | [Reference](https://doi.org/10.1093/bib/bbab549) | Snakemake; Bacterial ORF detection Benchmarking |
| RiboShape | [Code](https://sourceforge.net/projects/riboshape) | [Reference](https://doi.org/10.1093/bioinformatics/btw253) | Generation of Ribosome Profiles from sequence; MATLAB |
| RiboShape (different) | [Code](https://github.com/lulab/Riboshape) | [Reference]() | Workflow for analysis of RNA structure impact on translation |
| RiboFormer | [Code](https://github.com/lingxusb/Riboformer) | [Reference](https://doi.org/10.1038/s41467-024-46241-8) | Python; Transformer for Ribo-Seq Profile Prediction |
| Translatomer | Not Published Yet | [Reference](https://doi.org/10.1101/2024.02.26.582217) | Python; multimodal transformer; predicts cell-type-specific profiles |
| RiboGL | [Code](https://github.com/vam-sin/ribogl/) | [Reference](https://doi.org/10.1101/2024.04.08.588507) | Python; Ribosome Density prediction with GCN and BiLSTM |
#### Unsorted list:
- RCSU RS (https://doi.org/10.1093/dnares/dsw062)
- RiboStan (Ohler Lab) [Link](https://github.com/ohlerlab/RiboStan/tree/main)