Phillip Richmond's repositories
GenomeAnalysisModule
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
PrecisionHealthVirtualEnvironment
This is a virtual environment which contains databases, software, workflows, and workshops for Precision Health Data Analysis.
AnnotateVariants
This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.
Bioinformatics-Introductory-Analysis-Course
This repository contains course material for Phillip Richmond's Introduction to Bioinformatics Analysis Course
SV_Calling_And_Annotation
This repo details the SV annotation for Illumina WGS data.
ALD_Modifier_Project
This repository houses scripts for analysis and plotting of the ALD Modifier Project headed by Clara van Karnebeek
Annotate_CNVs
This is a repo that contains recipes for CNV annotation
AnnotSV
Annotation and Ranking of Structural Variation
arcsv
Complex structural variant detection from WGS data
arcsv-docker
A docker container for the arc-sv tool
ArrayFromWGS
This repository contains code and instructions for setting up the ArrayFromWGS analysis, which extracts read-depth and genotype information from curated genomic probe sets.
BuildControlCohort
This repo is for building a control cohort for WGS and RNAseq.
BuildInHouseDB
This set of scripts will build an in-house database once you deposit VCF files into a directory.
choosealicense.com
A site to provide non-judgmental guidance on choosing a license for your open source project
ComputeCanada_EOT
This is a repository for the Education, Outreach and Training tutorials offered by Compute Canada
ExpansionHunterDenovo
A suite of tools for detecting expansions of short tandem repeats
FlexTyper-Manuscript-Analysis
This is the repository for the analysis of data in the FlexTyper project
FlexTyper_manuscript
A repository for the code and analysis for the FlexTyper paper
HaplotypingUtils
Some scripts and utilities for haplotyping analysis collaboration with Hayden lab.
old-website.io
This is the website for Phillip A Richmond. I guess to keep some of my stuff in one spot?
phillip-a-richmond.github.io
personal website
RGDModule
An interactive website utilizing synthetic rare genetic disease scenarios to teach about the process of variant/gene prioritization in rare disease diagnosis.
scRNAseq-docker
This is a docker container for use in scRNAseq analysis.
stix-docker
Dockerfile for Ryan Layer's stix sv annotator + associated tools
varsim
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
WassermanLabWebsite
Allan Lab website
website-retired-2022
Personal website
Yeast-Ty1-TIPseq-Analysis
This is the repository for code pertaining to the analysis of yeast Ty1 sequencing data.