chr1swallace
Statisitician using genomics to understand immune-mediated diseases. Github hosts mainly R packages to do statistical analysis of genetic data.
University of CambridgeCambridge, UK
Pinned Repositories
annotSnpStats
repo for R package annotSnpStats
chr1swallace.github.io
Group website
coloc
Repo for the R package coloc
coloc-priors-mask-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.
GUESSFM
R package for fine mapping genetic associations in imputed GWAS data.
random-functions
R functions for which I want some version control
simGWAS
Simulating the expected output from a GWAS with a given causal model.
snphap
Copy of snphap source, written by David Clayton, put here because existing website is closing.
snpStatsWriter
Repo for the R package snpStatsWriter
chr1swallace's Repositories
chr1swallace/coloc
Repo for the R package coloc
chr1swallace/simGWAS
Simulating the expected output from a GWAS with a given causal model.
chr1swallace/GUESSFM
R package for fine mapping genetic associations in imputed GWAS data.
chr1swallace/annotSnpStats
repo for R package annotSnpStats
chr1swallace/chr1swallace.github.io
Group website
chr1swallace/coloc-susie-paper
chr1swallace/ibd-ets2-analysis
chr1swallace/slurmer
Interact with slurm
chr1swallace/doom
chr1swallace/PAH-simulations
simulations to examine stratified approach to FDR testing in small numbers of hypotheses
chr1swallace/acr-p-values
permutation to adjust optiomistic p values
chr1swallace/Autoimmunity_in_PAH
Autoimmunity in Pulmonary Arterial Hypertension
chr1swallace/cd-finemapping-scripts
chr1swallace/chr1swallace
README on main github page
chr1swallace/clusteringPublicGeneExpr
chr1swallace/cophescan
chr1swallace/cophescan-manuscript-sim-summary-data
chr1swallace/corrcoverage-v1
Repo for corrcoverage package
chr1swallace/data-sharing-search
code used in https://www.biorxiv.org/content/10.1101/2022.09.27.509657v2
chr1swallace/DPMUnc
chr1swallace/DPMUnc_GWAS
chr1swallace/DPMUnc_simulations
chr1swallace/elisa-paper
chr1swallace/emacs-from-scratch
chr1swallace/FasterCliquePercolation
chr1swallace/FastJaccard
fast Jaccard indexes for long lists of character vectors
chr1swallace/fgsea-search
chr1swallace/gwas-sharing
carrots
chr1swallace/manteltest
some code to run a Mantel test of similarity between matrices
chr1swallace/shaprs
Leveraging shared genetic effects to improve genetic risk prediction for related diseases