Matthew S Lyon's repositories
GermlineEnrichment
Variant calling pipeline for germline enrichment NGS data
SomaticAmplicon
NGS pipeline for somatic variant calling from amplicon datasets
VariantDatabase
Neo4j, AngularJS, NodeJS, ExpressJS stack for large scale variant storage and analysis
VariantReporterSpark
Apache Spark application for filtering and reporting clinically relevant variants
AmpliconRealigner
Tool for realigning soft-clipped bases from amplicon reads
IlluminaQC
Shell script for BCL to uBAM, QC and analysis launch
python-sample-send-mail
send email from Python via Microsoft Graph
QUAIL
A unified framework to estimate genetic effects on the variance of quantitative traits
scholar_patents
A parser for Google Scholar, written in Python
SoftClipPCRPrimer
Tool for soft-clipping PCR primers based on alignment location
spatial
Neo4j Spatial is a library of utilities for Neo4j that faciliates the enabling of spatial operations on data. In particular you can add spatial indexes to already located data, and perform spatial operations on the data like searching for data within specified regions or within a specified distance of a point of interest. In addition classes are provided to expose the data to geotools and thereby to geotools enabled applications like geoserver and uDig.
try-manubot
A repository to practice contributing to a Manubot manuscript
TwoSampleMR
R package for performing 2-sample MR using MR-Base database
vagrant-docker-compose
A Vagrant provisioner for docker compose.
vgraph
vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph representation of genomic variants in to precisely compare complex variants that are refractory to comparison by conventional comparison methods.