Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome
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
ORFquant: https://github.com/lcalviell/ORFquant
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
