@ThorntonLab

Kevin Thornton's lab group at UC Irvine

Kevin Thornton's lab

  • How we got CUDA installed and Tensor Flow working with GPU

    2 Updated Aug 27, 2018
  • Example using simulated data.

    Shell 1 Updated Aug 26, 2018
  • Website for Kevin Thornton's lab at UC Irvine

    CSS 1 Updated Jul 29, 2018
  • IBD regions identified in DGRP lines by Cridland et al. (2013) doi: 10.1093/molbev/mst129

    1 Updated Apr 3, 2018
  • Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.

    Python 5 GPL-3.0 Updated Mar 21, 2018
  • A PLINK-based implementation of the "ESM" test from Thornton, Foran and Long (2013)

    Shell 1 1 Updated Jun 14, 2017
  • Notes for reading group on Burger's 2000 book.

    HTML Updated Apr 25, 2017
  • Materials for EE283

    HTML 1 Updated Feb 6, 2017
  • Tips and tricks we've learned during the course of research in computational biology.

    Updated Sep 14, 2016
  • Various scripts, etc., for helping write papers.

    Shell Updated Aug 18, 2016
  • Shell 1 Updated Jun 23, 2016
  • Shell scripts to download raw data for simulans and yakuba resequencing

    Shell Updated Apr 29, 2016
  • Population Genomic Data and SNPs for Drosophila yakuba and Drosophila simulans

    Updated Jun 17, 2015
  • Tips and tricks for using SGE queues (and related systems like OGE). Focused on the UCI HPC system, but much will apply elsewhere.

    Updated Feb 11, 2015
  • Simulation code from Thornton, Foran and Long (2013) PloS Genetics

    C++ Updated Jan 2, 2015
  • Methods for genome annotation using paired-end RNA-seq data

    Shell 1 1 Updated Oct 16, 2014
  • TE presence/absence calling pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129

    C++ 1 Updated Oct 8, 2014
  • TE annotation pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129

    Perl 1 Updated Oct 8, 2014
  • Alignments from Thornton and Long, doi: 10.1093/molbev/msi015

    Updated Oct 8, 2014
  • Alignments from Thornton et al. (2006), Genome Research

    Updated Oct 8, 2014
  • Various files related to writing R01s in LaTeX.

    TeX Updated Sep 14, 2014
  • GFF files coming out of our reannotation efforts

    1 Updated Aug 20, 2014
  • Processing RNA-seq data from Susan Lott

    Updated Jul 17, 2014
  • Quick intro to github. Contents for UCI journal club on the topic

    Updated Jun 20, 2014
  • Hints, tips, and tricks for dealing with LaTeX submissions to arXiv.org

    Updated Jun 20, 2014
  • Aligning PACbio data to a reference. (Specific for data received from UCI core)

    Updated May 23, 2014
  • Notes for various approaches to de novo genome assembly

    Shell 1 Updated Apr 2, 2014
  • Supplementary material related to Rogers et al.

    1 Updated Mar 31, 2014