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awesome-riboseq

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A list of bioinformatic tools for working with Ribo-Seq data

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# 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

- [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)

awesome-riboseq

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