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How we got CUDA installed and Tensor Flow working with GPU
Example using simulated data.
Website for Kevin Thornton's lab at UC Irvine
IBD regions identified in DGRP lines by Cridland et al. (2013) doi: 10.1093/molbev/mst129
Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.
A PLINK-based implementation of the "ESM" test from Thornton, Foran and Long (2013)
Notes for reading group on Burger's 2000 book.
Materials for EE283
Tips and tricks we've learned during the course of research in computational biology.
Various scripts, etc., for helping write papers.
Shell scripts to download raw data for simulans and yakuba resequencing
Population Genomic Data and SNPs for Drosophila yakuba and Drosophila simulans
Tips and tricks for using SGE queues (and related systems like OGE). Focused on the UCI HPC system, but much will apply elsewhere.
Simulation code from Thornton, Foran and Long (2013) PloS Genetics
Methods for genome annotation using paired-end RNA-seq data
TE presence/absence calling pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129
TE annotation pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129
Alignments from Thornton and Long, doi: 10.1093/molbev/msi015
Alignments from Thornton et al. (2006), Genome Research
Various files related to writing R01s in LaTeX.
GFF files coming out of our reannotation efforts
Processing RNA-seq data from Susan Lott
Quick intro to github. Contents for UCI journal club on the topic
Hints, tips, and tricks for dealing with LaTeX submissions to arXiv.org
Aligning PACbio data to a reference. (Specific for data received from UCI core)
Notes for various approaches to de novo genome assembly
Supplementary material related to Rogers et al.