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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: 6 days ago
JSON representation

  • Data Resources and Visualisation Environments

    • Code
    • Code
    • Code
    • Code
    • 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 |
    • Code
    • 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 |
    • Code
    • Code - 016-3278-x) | Written in Python; Packaged on PyPi; Analysis |
    • Code
    • Code - to-end |
    • Code
    • Code
    • Code
    • 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 |
    • Code
    • Code
    • 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

    • Code
    • Code
    • Code
    • Code - 019-42348-x) | Written in Python; Paper contains comparison of methods |
    • Code
    • 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 |
    • Code
    • Code - sites |
    • Code
    • Code
    • Code

  • 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 |
    • Code
    • Code - 019-3244-0) | Python; RNA-Seq free Isoform level quantification |
    • Code
    • 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 |
Programming Languages
Python 42 R 22 Perl 5 Shell 3 HTML 3 C++ 2 Jupyter Notebook 2 PureBasic 1 Perl 6 1 PHP 1
Categories
Data Processing and Analysis 28 ORF Calling 24 Misc 11 Isoform Level Analysis 8 Data Resources and Visualisation Environments 8 Differential Analysis 8 Quality Control 6 Offset Determination 6 ORF Databases 5 Occupancy Analysis 3 Ribo-Seq Simulation 3 Pause Prediction 2 Frameshift Detection 1
Sub Categories
Keywords
ribosome-profiling 12 bioinformatics 8 riboseq 5 ribosome 4 ngs 3 orfs 3 python 2 snakemake 2 translation 2 ribo-seq 2 pyplot 1 perl 1 mqc 1 mappingqc 1 mapping 1 website 1 shiny-apps 1 r 1 polysome-profiling 1 riborex 1 differential-translation 1 profiling 1 bioinformatics-scripts 1 visualisation 1 lstm 1 interpretability 1 graph-neural-networks 1 generalized-linear-models 1 quantification 1 differential-splicing-analysis 1 prokaryotes 1 uorfs 1 python3 1 genomics 1 translation-initiation-site 1 bam-files 1 peptides 1 translation-regulation 1 ribosome-profiling-data 1 ridge-regression 1 random-forest 1 glmnet 1 glm 1 quality-control 1 rna-seq 1