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cadzow2017_ukbiobank_gout

Code used in the analysis of https://arthritis-research.biomedcentral.com/articles/10.1186/s13075-017-1390-1

cetp-project

commonworkflows

A repository to document common workflows or computational protocols (for example merging and subsetting VCF files).

conditional-analysis-of-kottgen

Based on Yang et al 2012 nature genetics paper

eqtl_project

Development of a central data warehouse for eQTL and gene expression data. Including a SHINY interface to perform lookups and basic exploration.

exporatorygenomes

Exploratory and visual analytical tools for plant genomes.

geneexpressionanalysis

Shiny app for basic exploration of gene expression datasets

genomedb

GenomeDB is a generic database schema for genome-wide summary datasets. The goal is to be able to provide a general abstraction suited to any form of genome analysis, for example GWAS, QTL, gene expression, regulatory peaks...

genomicpred

git_rstudio_example

glida

GLIDA is a tool to help analyse patterns of LD. Primarily visual and exploratory-based, with the ability to add gene annotations.

gsclustbrowse

Shiny app for browsing the exported intensities from Genome Studio

gtexeda

Visualisation and exploration of gene expression data from GTEx, using R's data.table package.

gwasdb

Database to store summary results from GWAS

gwaspipeline

A basic GWAS analyses workflow. Worked examples provided in rendered markdown.

gwrangle

Helpful code, scripts and functions fro wrangling genomic datasets

human_genomics_pipeline

A simple Snakemake workflow to process paired-end sequencing data (WGS) using bwa/GATK4.

impute

kottgen_reseqanalysis

Various resequencing trials with the Kottgen data

ldcalculator

Shiny Interface for the calculation of Linkage Disequilibrium.

merrimandw

merrimanlab.github.io

merrimanr

An R package containing useful functions

nesi_gatk

workflow for GATK on NeSI

old_website

Lab website

pcaplotting

PCA plotting app

penncnv

Copy number vaiation detection from SNP arrays

pleiotropic_effects_of_abcg2_studentship

R scripts detailing file organisation/subsetting and regression commands used in the studentship.

prs-project

Repository for all code related to my polygenic risk score project

pseqc

Resequencing QC Pipeline.