Ribotools

Introduction

Ribotools is a toolbox for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) data. Ribotools can be used in standalone mode or in combination with Rp-Bp for Ribo-seq quality control, open reading frames (ORFs) discovery, translation efficiency (TE), and differential expression (DE) analyses.

Ribotools uses Rp-Bp for periodicity estimation and follows the same alignment workflow, directory structure, and naming convention. It uses HTSeq for abundance estimation and DESeq2 for statistical testing.

• Getting started
• Installation
• User guide
  • How to add a config file
  • How to prepare annotations
  • How to estimate abundance
  • How to estimate TE
  • How to estimate DE
  • How to use Ribo-seq ORFs
  • Default parameters
• Tutorials
  • Run the TE pipeline
• Frequently asked questions
• API
  • run-htseq-workflow
  • get-gtf-from-predictions
  • get-sample-table
  • run-tea
  • run-dea