Ribo-seq分析综述

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

image.png

Resources

Preprocessing and Quality Control

ⁱCutadapt: http://cutadapt.readthedocs.io/en/stable/index.html

ⁱⁱPlastid: http://plastid.readthedocs.io/en/latest/

ⁱⁱⁱRfoot: www.broadinstitute.org/∼zheji/software/Rfoot.0.1.tar.gz

^ivRiboGalaxy: http://ribogalaxy.ucc.ie

^vRiboProfiling: https://bioconductor.org/packages/release/bioc/html/RiboProfiling.html

^viRiboSeqR: http://bioconductor.org/packages/release/bioc/html/riboSeqR.html

^viiRiboTools: https://testtoolshed.g2.bx.psu.edu/repository?repository_id=d5063de8c6e62bf2

^viiiRUST: http://lapti.ucc.ie/rust/

^ixSTAR: https://github.com/alexdobin/STAR

Databases

^xGWIPS-viz: http://gwips.ucc.ie

^xiRPFdb: http://sysbio.sysu.edu.cn/rpfdb/index.html

ORF Finding

^xiiORF-Rater: https://github.com/alexfields/ORF-RATER

^xiiiRb-Bp: https://github.com/dieterich-lab/rp-bp

^xivRiboHMM: https://github.com/rajanil/riboHMM

^xvRibORF: https://personal.broadinstitute.org/zheji/software/RibORF.html

^xviRiboTaper: https://ohlerlab.mdc-berlin.de/software/

^xviiRRS: www.lncrna-test.caltech.edu/software.php

^xviiiSPECtre: https://github.com/mills-lab/spectre

Differential Analysis

^xixAnota: www.bioconductor.org/packages/release/bioc/html/anota.html

^xxBabel: https://cran.r-project.org/web/packages/babel/index.html

^xxiRiboDiff: https://github.com/ratschlab/RiboDiff

^xxiiRiborex: https://github.com/smithlabcode/riborex

^xxiiiXtail: https://github.com/xryanglab/xtail