pasted

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

gw_meta_analysis_low_muscle_strength

Analysis code and processing stages for Genome-Wide meta-analysis of low grip strength in older people.

simple_bash_pipeline

Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. Originally developed as Masters in Bioinformatics project @ University of Exeter

targeted_sequencing_pipeline

Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab.

variant_parser

Selects possible pathogenic variants from an Alamut output

2017-07-14-exeter-swc

action_manager

Small example API

mosaic_clusterer

Uses SciKit Learn library's Mean Shift implementation to draw a chart of mosaic variants

virtual_parser

Virtual panel parser with ruleset for pathogenic variants, for use with Cellbase annotated variants

bioruby

bioruby

bolt_parser

Parser to merge multiple external annotations with BOLT-LMM outputs

ChAMP

cooccurrence_matrix

Basic Co-occurrence matrix testbed in Python

dendroscope_parser

Very old dendroscope parser and annotator

dynapenia_analysis_plan

ge_code_test

gene_coverage_report

Small application to demostrate Biomart, Bio-SamTools (ruby wrapper around Samtools) and Nyaplot graphs

gtfparse

Parsing tools for GTF (gene transfer format) files

hgvs

HGVS variant name parsing and generation

hus-sys

Heamolytic-Uremic Syndrome System

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

kerplink

Plink pipeline for GWAS Additive / Recessive models

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

open_target_query

plink_parser

PLINK 1.9 parser and filter

spreadsheet

The Ruby Spreadsheet by ywesee GmbH

starlims_report_generator

Example report generator for StarLIMS

test_project

transpose_ped

trio_generator

Example workflow to generate a trio VCF from parental data