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added differential translation section
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JackCurragh committed Jan 16, 2023
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Expand Up @@ -36,9 +36,14 @@ A list of bioinformatic tools for working with Ribo-Seq data. Please feel free t


## Differential Translation
| Tool | Code | Reference | Note(s) |
| ------------- | ------------- | ------------- | ------------- |
| | [Code]() | [Reference]() | |
| 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 |



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- RiboZINB (translated isoform)
- Ribofy (https://github.com/ncrnalab/ribofy)
- orfRater
-
- RiboDiPa

[L](http://rnainformatics.org.cn/RiboToolkit/links.php)

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