chr1swallace/chr1swallace.github.io

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chr1swallace/chr1swallace.github.io

chr1swallace

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Group website

coloc

Repo for the R package coloc

random-functions

R functions for which I want some version control

GUESSFM

R package for fine mapping genetic associations in imputed GWAS data.

coloc-priors-mask-paper

snphap

Copy of snphap source, written by David Clayton, put here because existing website is closing.

coloc-susie-paper

finemap-psa

simple fine mapping script in R used as the basis for analyses in Bowes et. al (2015), Dense genotyping of immune-related susceptibility loci reveals new insights into the genetics of psoriatic arthritis.

fm-priors

simulations to consider effect of varying prior distribution and variance in single causal variant fine mapping

simgwas-paper

calculations run for our simGWAS paper

slurmer

Interact with slurm

annotSnpStats

repo for R package annotSnpStats

ibd-ets2-analysis

fitmix

fix mixture prior for eqtl effects

caller

cluster beta/gaussian mixture data

condpp

R code used to explore appropriate p value thresholds for calling genetic association in one disease given genomewide significant genetic association at the same SNP in a related disease in the T1D ImmunoChip paper (Onengut et al, in press)

PAH-simulations

simulations to examine stratified approach to FDR testing in small numbers of hypotheses

writing

Academic writing styles

doom