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
coloc
Repo for the R package coloc
coloc-priors-mask-paper
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.
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/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.
chr1swallace/snphap
Copy of snphap source, written by David Clayton, put here because existing website is closing.
chr1swallace/writing
Academic writing styles
chr1swallace/snpStatsWriter
Repo for the R package snpStatsWriter
chr1swallace/abcGWAS
Using Approximate Bayesian Computation to fine map causal variants from GWAS summary data.
chr1swallace/allanlab
Allan Lab website
chr1swallace/cd4-pchic
chr1swallace/cFDR
faster cFDR using Rcpp, but not adaptation for common controls
chr1swallace/cFDR-common-controls
This repository contains R functions to compute the 'Conditional False Discovery Rate', a method to analyse genome-wide association studies (GWAS) for related diseases originally proposed by Andreasson et al (2013), in the case where the two GWAS have shared controls.These functions widen the scope of the existing technique and enable improved power.
chr1swallace/CHIGP
Capture Hi-C gene prioritiser
chr1swallace/cluster-power
Power calcs for cluster
chr1swallace/colocCommonControl
chr1swallace/credibleset_thesis
chr1swallace/cvs
chr1swallace/cvs-approx
chr1swallace/dotwhisker
Dot-and-Whisker Plots of Regression Results
chr1swallace/genomic.autocorr
Use block bootstrap to allow for spatial dependencies in genomic data used in glms
chr1swallace/ggdendro
Tools to extract dendrogram plot data for use with ggplot
chr1swallace/junk
chr1swallace/lyons-et-al
code to support fine mapping in Lyon's et al
chr1swallace/Martin-2015-Figure3
Code to create Figure 3 in Martin et al, 2015
chr1swallace/MFM-analysis
chr1swallace/MFM-paper
chr1swallace/orgmode-accessories
Add ons for orgmode
chr1swallace/scripts-general-use
chr1swallace/simBasis
misc code to simulate basis scenarios
chr1swallace/snpHaps
chr1swallace/StarWarsIntroCreator
Create your own Star Wars intro.
chr1swallace/subtest
A package for testing for differential genetic basis between two putative disease subtypes
chr1swallace/TibsPower
Power calculations for microarray expts using the Tibshirani (2006) method