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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
JSON representation
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Data Resources and Visualisation Environments
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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
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- 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
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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
- Code - gene analysis on microbial (Bacteria and Archaea) data |
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Differential Analysis
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Quality Control
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Offset Determination
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ORF Calling
- Reference
- Code
- Code - Seq + SD sequence |
- Code
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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 |
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- Code
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ORF Databases
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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 |
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Misc
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Ribo-Seq Simulation
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Occupancy Analysis
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Pause Prediction
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Frameshift Detection
- Code - 023-05602-8) | Python; HMM; detects many different alt-ORF types |
Programming Languages
Categories
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