Notebooks for the analysis of Ribo-Seq QC Metrics

A command-line utility for the generation of comprehensive reports on ribosome profiling (Ribo-Seq) dataset quality

Command line implementation of the Trips-Viz ORF calling method

Implementation of the Ribosome Decision Graph Concept

A list of bioinformatic tools for working with Ribo-Seq data

Nextflow pipeline for running RiboMetric on Genomic BAMs (as per rdp.ucc.ie)

repo for automated processing of Ribo-Seq (and associated RNA-seq) data

Ribosome Descision Graph viewer in the browser

Pipeline used to detect ORFs from Mouse Ribo-Seq during time at EBI/Gencode

Contains methods used to create test data (primarily for nf-core modules)

Modules directory for custom nf-core modules that cannot be added to main nf-core

Standalone Nextflow Pipeline for the annotation of Selenoproteins @ Ensmbl

Home of code for recode.ucc.ie legacy homepage

Test what effect subssampling of a run has on QC

Fetch FASTQ files, clean and collapse duplicated reads

Automated construction of bowtie indices

Combine collapsed read files into a single DB

Template repository for setting up new Nextflow pipelines

Projecting the growth of RiboSeq.Org

Assess the degree to which a given set of genomic ranges have Ribo-Seq support

Code for the exploration of expressed proteofroms

Scripts for exploring the presence of overlapping ORFs in reference transcriptomes