Garan Jones's repositories
gtfparse
Parsing tools for GTF (gene transfer format) files
dendroscope_parser
Very old dendroscope parser and annotator
kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
spreadsheet
The Ruby Spreadsheet by ywesee GmbH
bioruby
bioruby
gw_meta_analysis_low_muscle_strength
Analysis code and processing stages for Genome-Wide meta-analysis of low grip strength in older people.
kerplink
Plink pipeline for GWAS Additive / Recessive models
plink_parser
PLINK 1.9 parser and filter
variant_parser
Selects possible pathogenic variants from an Alamut output
targeted_sequencing_pipeline
Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab.
bolt_parser
Parser to merge multiple external annotations with BOLT-LMM outputs
virtual_parser
Virtual panel parser with ruleset for pathogenic variants, for use with Cellbase annotated variants
cooccurrence_matrix
Basic Co-occurrence matrix testbed in Python
clinical_variant_database
Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset. Originally developed as part of a Masters in Bioinformatics project @ University of Exeter
action_manager
Small example API
starlims_report_generator
Example report generator for StarLIMS
mosaic_clusterer
Uses SciKit Learn library's Mean Shift implementation to draw a chart of mosaic variants
trio_generator
Example workflow to generate a trio VCF from parental data
gene_coverage_report
Small application to demostrate Biomart, Bio-SamTools (ruby wrapper around Samtools) and Nyaplot graphs
simple_bash_pipeline
Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. Originally developed as Masters in Bioinformatics project @ University of Exeter
hgvs
HGVS variant name parsing and generation
hus-sys
Heamolytic-Uremic Syndrome System