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2017-07-14-exeter-swc

action_manager

Small example API

biomart

A ruby API for interacting with Biomart services

biomart_query

Rough Biomart example generating Interval Lists from transcript Ids

bioruby

bioruby

bolt_parser

Parser to merge multiple external annotations with BOLT-LMM outputs

champ

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

closure_tree

Easily and efficiently make your ActiveRecord model support hierarchies

cooccurrence_matrix

Basic Co-occurrence matrix testbed in Python

dendroscope_parser

Very old dendroscope parser and annotator

dynapenia_analysis_plan

fastq-factory

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

gw_meta_analysis_low_muscle_strength

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

hgvs

HGVS variant name parsing and generation

hus-sys

Heamolytic-Uremic Syndrome System

jbrowse

A modern genome browser in JavaScript

kaiju

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

kerplink

Plink pipeline for GWAS Additive / Recessive models

mosaic_clusterer

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

multiqc

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

open_target_query

percolate

A parallel workflow management application.

plink_parser

PLINK 1.9 parser and filter

seqfrequency

Sequence frequency toy-app

simple_bash_pipeline

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

spreadsheet

The Ruby Spreadsheet by ywesee GmbH