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lbfgsb-matlab
A MATLAB interface for L-BFGS-Bvarbvs
Large-scale Bayesian variable selection for R and MATLAB.cfw
R code implementing QTL mapping of physiological, behavioral and gene expression phenotypes in Carworth Farms White (CFW) outbred mice.ppi-f1-gwas
R code implementing QTL mapping of prepulse inhibition phenotypes in F1 crosses of common inbred mouse strainspcarbo
Source code I have shared and analyses I have done.lps
Analysis of LPS (bulk) RNA-seq data from Chevrier lab.QTLRel
R package for mapping quantitative trait loci in experimental crosses such as advanced intercross lines where relatedness among individuals should not be ignored.dotfiles
Files for setting up shell environment on my MacBook and the compute clusters I regularly use.bmapathway
MATLAB source code to accompany the PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease".neuron
Code and data implementing statistical analyses for Neuron manuscript, "Genetic background limits generalizability of genotype-phenotype relationships"R-survival-large-scale
Materials for tutorial, "A survival guide to large-scale data analysis in R."lgsmfear
R code implementing QTL mapping of fear conditioning traits in LG/J x SM/J mouse advanced intercross line.genotype
Various scripts and functions for manipulating genetic data.kyoto
Module for 2014 Kyoto Course on Bioinformaticsb6d2muscle
R code implementing QTL mapping of hindlimb muscle weights in C57BL/6J ("B6") x DBA/2J ("D2") mouse advanced intercross line.mr-ash
A simple implementation of the "multiple regression adaptive shrinkage" model, with examples.pcarbo.github.io
Personal websitemixopt-experiments
Empirical comparisons of algorithms for solving the "mixture distribution" optimization problem.rrqr
Toy R package implementing the rank-revealing QR decomposition using RcppEigen.vardemo
Small demonstration of importance sampling, Laplace's method and a variational approximation for logistic regressioncolab
Explorations of the Google Colaboratory.genetic-data-analysis-rcc-1
Research Computing Center introduction to analysis and visualization of genetic data, Part 1genetic-data-analysis-rcc-2
Research Computing Center introduction to analysis and visualization of genetic data, Part 2breedail
R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspringgwas-demos
Some R code used to illustrate basic concepts in genome-wide association studies.Love Open Source and this site? Check out how you can help us