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awesome-riboseq

A list of bioinformatic tools for working with Ribo-Seq data
https://github.com/JackCurragh/awesome-riboseq

Last synced: 1 day ago
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  • Data Resources and Visualisation Environments

    • Code
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    • Code - 019-2706-8) | Command line app; Genomic |
    • Code
    • Code - 021-00824-4) | R; Similar transcript plotting to RiboCrypt (w/ multiple isoforms)|
    • Code
  • Data Processing and Analysis

    • Code - 018-4912-6) | Written in python |
    • Code
    • Code - 016-1241-0) | Written in R; Available on Bioc; End-to-end |
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    • Code - to-end |
    • Code - to-end |
    • Link
    • Code - to-end processing and analysis |
    • Code - 019-5700-7) | Written in R; Available as web app |
    • Code - to-end |
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    • Code - 016-3278-x) | Written in Python; Packaged on PyPi; Analysis |
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    • Code - to-end |
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    • Code - 021-03887-4) | Publication Code; Nextflow; R for figures |
    • Code - 020-9536-2) | Bacterial Ribo-Seq pipeline; Shell; Python; R |
    • Code - Seq Data Processing; Snakemake; Paired with RiboSeeker |
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    • Code - to-end ribo-seq analysis |
    • Code - 023-01141-9) | R; Regression based tools for Ribo-Seq analysis Heterogeneity |
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    • Code - gene analysis on microbial (Bacteria and Archaea) data |
  • Differential Analysis

  • Quality Control

  • Offset Determination

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    • Code - 019-42348-x) | Written in Python; Paper contains comparison of methods |
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    • Code - 021-04068-w) | Written in Python; Django app in docker image; GUI for Integer Programming method above |
  • ORF Calling

    • Reference
    • Code
    • Code - Seq + SD sequence |
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    • Code - 017-01981-8) | Python; TI-seq (TIS Hunter); Supports differential initiation analysis |
    • Code
    • Code - to-end pipeline; Bayesian Periodic fragment length and ribosome P-site offset Selection |
    • Code - 016-1355-4) | Python; Spectral analysis of sliding windows |
    • Code - approach; Methods unclear as paper describes regression |
    • Code - Seq; Conservation based; One 5' UTR at a time |
    • Code - to-end; Plastid + ORFscore |
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    • Code - sites |
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  • ORF Databases

    • Link
    • Link - Seq + Mass Spec; Polycistronic gene models |
    • Link
    • Link - 020-00167-4) | Aggregated database of OpenProt and sORFs.org; Nice UI |
    • Link
  • Isoform Level Analysis

    • Code - 021-04192-7) | Perl; RSEM: Isoform level analysis |
    • Code
    • Code - 020-0450-4) | R; Isoform level translation quantification of ORFs |
    • Code - 020-15634-w) | Python, Shell; Isoform level quantification extending Ribomap |
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    • Code - 019-3244-0) | Python; RNA-Seq free Isoform level quantification |
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    • Code - Input Multi-Output full isoform density prediction |
  • Misc

  • Ribo-Seq Simulation

  • Occupancy Analysis

  • Pause Prediction

  • Frameshift Detection

    • Code - 023-05602-8) | Python; HMM; detects many different alt-ORF types |