JackCurragh
PhD Candidate with SFI funded CRT Genomic Data Science (background in Genetics). Researching the accurate annotation and visualisation of protein coding loci
CRT Genomic Data Science University College Cork
Pinned Repositories
awesome-riboseq
A list of bioinformatic tools for working with Ribo-Seq data
Collapse-FASTQ
Fetch FASTQ files, clean and collapse duplicated reads
ensembl-miRNA-nf
miRNA Detection workflow developed for genebuild team at Ensembl
RDG
Implementation of the Ribosome Decision Graph Concept
RiboMetric
A command-line utility for the generation of comprehensive reports on ribosome profiling (Ribo-Seq) dataset quality
Riboseq-checker
Organism agnostic python program to check the 3' periodicity of a Ribo-Seq sample
TranslonPredictor
Command line implementation of the Trips-Viz ORF calling method
JackCurragh's Repositories
JackCurragh/awesome-riboseq
A list of bioinformatic tools for working with Ribo-Seq data
JackCurragh/RDG
Implementation of the Ribosome Decision Graph Concept
JackCurragh/TranslonPredictor
Command line implementation of the Trips-Viz ORF calling method
JackCurragh/Animating-RDGs
JackCurragh/Collapse-FASTQ
Fetch FASTQ files, clean and collapse duplicated reads
JackCurragh/RiboMetric
A command-line utility for the generation of comprehensive reports on ribosome profiling (Ribo-Seq) dataset quality
JackCurragh/riboseq_data_processing
repo for automated processing of Ribo-Seq (and associated RNA-seq) data
JackCurragh/custom-nf-core-modules
Modules directory for custom nf-core modules that cannot be added to main nf-core
JackCurragh/dotfiles
A repo for my dotfiles
JackCurragh/ensembl-selenoproteins
Standalone Nextflow Pipeline for the annotation of Selenoproteins @ Ensmbl
JackCurragh/gencode-mouse-orfs
Pipeline used to detect ORFs from Mouse Ribo-Seq during time at EBI/Gencode
JackCurragh/index-construction
Automated construction of bowtie indices
JackCurragh/jackcurragh.github.io
Jack Tierney's GitHub Projects
JackCurragh/LAPTI-Docs
JackCurragh/LLM
JackCurragh/mappability-diff
Compare mappability tracks
JackCurragh/Metric-Analysis
Notebooks for the analysis of Ribo-Seq QC Metrics
JackCurragh/nextflow-plugins
Nextflow plugins index repository
JackCurragh/Nextflow-Template
Template repository for setting up new Nextflow pipelines
JackCurragh/nf-core-test-datasets
Test data to be used for automated testing with the nf-core pipelines
JackCurragh/RDG-VEP
Using RDGs to investigate the impact of sequence variants
JackCurragh/RDG-Viewer
Ribosome Descision Graph viewer in the browser
JackCurragh/Read-File-Combination
Combine collapsed read files into a single DB
JackCurragh/recode
Home of code for recode.ucc.ie legacy homepage
JackCurragh/RiboCrypt
JackCurragh/RiboMetric-nf
Nextflow pipeline for running RiboMetric on Genomic BAMs (as per rdp.ucc.ie)
JackCurragh/riboseqorg_metadata
Ribo-seq metadata standardization for RiboCrypt and Riboseq.org
JackCurragh/sample-dataset-creation
Contains methods used to create test data (primarily for nf-core modules)
JackCurragh/Subsample-Effect-On-QC
Test what effect subssampling of a run has on QC
JackCurragh/Trips-Viz-Scripts
Refactored scripts for Trips-Viz