pcarbo/dotfiles

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Created about 8 years ago
Updated almost 7 years ago

pcarbo/dotfiles

pcarbo

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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

varbvs

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 strains

pcarbo

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.

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 Bioinformatics

b6d2muscle

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 website

mixopt-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 regression

colab

Explorations of the Google Colaboratory.

Jupyter Notebook

mr-mash

A simple implementation of the multivariate multiple regression method with adaptive shrinkage priors ("mr-mash"), with examples.

genetic-data-analysis-rcc-1

Research Computing Center introduction to analysis and visualization of genetic data, Part 1

genetic-data-analysis-rcc-2

Research Computing Center introduction to analysis and visualization of genetic data, Part 2

breedail

R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring

gwas-demos

Some R code used to illustrate basic concepts in genome-wide association studies.