pcarbo
Research Assistant Prof, Human Genetics, U. Chicago; previously, Staff Scientist at Ancestry, postdoc & HFSP fellow at U. Chicago, & Ph.D. at UBC
University of ChicagoChicago, IL
Pinned Repositories
cfw
R code implementing QTL mapping of physiological, behavioral and gene expression phenotypes in Carworth Farms White (CFW) outbred mice.
dotfiles
Files for setting up shell environment on my MacBook and the compute clusters I regularly use.
lbfgsb-matlab
A MATLAB interface for L-BFGS-B
lps
Analysis of LPS (bulk) RNA-seq data from Chevrier lab.
pcarbo
Source code I have shared and analyses I have done.
ppi-f1-gwas
R code implementing QTL mapping of prepulse inhibition phenotypes in F1 crosses of common inbred mouse strains
varbvs
Large-scale Bayesian variable selection for R and MATLAB.
fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
mixsqp
R package for fast maximum-likelihood estimation of mixture proportions using SQP.
workflowr
Organize your project into a research website
pcarbo's Repositories
pcarbo/lbfgsb-matlab
A MATLAB interface for L-BFGS-B
pcarbo/cfw
R code implementing QTL mapping of physiological, behavioral and gene expression phenotypes in Carworth Farms White (CFW) outbred mice.
pcarbo/ppi-f1-gwas
R code implementing QTL mapping of prepulse inhibition phenotypes in F1 crosses of common inbred mouse strains
pcarbo/QTLRel
R package for mapping quantitative trait loci in experimental crosses such as advanced intercross lines where relatedness among individuals should not be ignored.
pcarbo/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".
pcarbo/lgsmfear
R code implementing QTL mapping of fear conditioning traits in LG/J x SM/J mouse advanced intercross line.
pcarbo/neuron
Code and data implementing statistical analyses for Neuron manuscript, "Genetic background limits generalizability of genotype-phenotype relationships"
pcarbo/b6d2muscle
R code implementing QTL mapping of hindlimb muscle weights in C57BL/6J ("B6") x DBA/2J ("D2") mouse advanced intercross line.
pcarbo/genotype
Various scripts and functions for manipulating genetic data.
pcarbo/kyoto
Module for 2014 Kyoto Course on Bioinformatics
pcarbo/admixture
Simple accelerated EM implementation of the ADMIXTURE model in R, plus extensions.
pcarbo/breedail
R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring
pcarbo/genetic-data-analysis-rcc-1
Research Computing Center introduction to analysis and visualization of genetic data, Part 1
pcarbo/genetic-data-analysis-rcc-2
Research Computing Center introduction to analysis and visualization of genetic data, Part 2
pcarbo/mixopt-experiments
Empirical comparisons of algorithms for solving the "mixture distribution" optimization problem.
pcarbo/vardemo
Small demonstration of importance sampling, Laplace's method and a variational approximation for logistic regression
pcarbo/cehg16-workshop
Demos for AncestryDNA workshop at 2016 CEHG Symposium, Stanford University.
pcarbo/cfwlab
R package containing data from CFW genome-wide association study for use in courses.
pcarbo/extreme-deconvolution
Density estimation using Gaussian mixtures in the presence of noisy, heterogeneous and incomplete data
pcarbo/gtexresults_matrixash
Repo for reproducing GTEx results in Urbut et al, 2017 "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions"
pcarbo/GUESSFM
R package for fine mapping genetic associations in imputed GWAS data.
pcarbo/jekyll-bootstrap
experimenting with jekyll and bootstrap
pcarbo/myqtl
This is a "fork" of kbroman/qtl which I am using to explore & demo features of git & github.
pcarbo/R-adv-hum-genet
Topics on Data Analysis in R for University of Chicago Human Genetics trainees.
pcarbo/simple_site
Minimal tutorial on making a simple website with GitHub Pages
pcarbo/varbvs-vs-gemma
Experiments comparing varbvs and GEMMA.
pcarbo/varbvs-workflowr
Attempt at using workflowr to organize & publish some data analyses using varbvs.