Jack Tierney's repositories
awesome-riboseq
A list of bioinformatic tools for working with Ribo-Seq data
TripsViz-ORF-Detector
Command line implementation of the Trips-Viz ORF calling method
Collapse-FASTQ
Fetch FASTQ files, clean and collapse duplicated reads
RiboMetric
A command-line utility for the generation of comprehensive reports on ribosome profiling (Ribo-Seq) dataset quality
riboseq_data_processing
repo for automated processing of Ribo-Seq (and associated RNA-seq) data
custom-nf-core-modules
Modules directory for custom nf-core modules that cannot be added to main nf-core
ensembl-selenoproteins
Standalone Nextflow Pipeline for the annotation of Selenoproteins @ Ensmbl
gencode-mouse-orfs
Pipeline used to detect ORFs from Mouse Ribo-Seq during time at EBI/Gencode
index-construction
Automated construction of bowtie indices
jackcurragh.github.io
Jack Tierney's GitHub Projects
Metric-Analysis
Notebooks for the analysis of Ribo-Seq QC Metrics
nextflow-plugins
Nextflow plugins index repository
Nextflow-Template
Template repository for setting up new Nextflow pipelines
nf-core-riboseq
Initial setup of nf-core Ribo-Seq pipeline
nf-core-test-datasets
Test data to be used for automated testing with the nf-core pipelines
nf-core-website
Code and files for the main nf-core website.
overlapping-orfs
Scripts for exploring the presence of overlapping ORFs in reference transcriptomes
Proteoform-Exploration
Code for the exploration of expressed proteofroms
RDG-Viewer
Ribosome Descision Graph viewer in the browser
Read-File-Combination
Combine collapsed read files into a single DB
recode
Home of code for recode.ucc.ie legacy homepage
RiboMetric-nf
Nextflow pipeline for running RiboMetric on Genomic BAMs (as per rdp.ucc.ie)
RiboSeqOrg-Projections
Projecting the growth of RiboSeq.Org
riboseqorg_metadata
Ribo-seq metadata standardization for RiboCrypt and Riboseq.org
sample-dataset-creation
Contains methods used to create test data (primarily for nf-core modules)
Subsample-Effect-On-QC
Test what effect subssampling of a run has on QC
Translation-Checker
Assess the degree to which a given set of genomic ranges have Ribo-Seq support