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@ThorntonLab Kevin Thornton's lab group at UC Irvine

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    37 repositories

    • ThorntonLab.github.io

      Public
      Website for Kevin Thornton's lab at UC Irvine
      Astro
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•2•1•Updated Oct 14, 2024Oct 14, 2024

    • demes_post_code

      Public
      Code for blog post about demes
      Python
      •0•0•0•0•Updated Jan 3, 2023Jan 3, 2023

    • RMarkdown_manuscript_template

      Public template
      Template for an article written using RMarkdown
      TeX
      •1•1•1•1•Updated Oct 27, 2022Oct 27, 2022

    • remark_slides_template

      Public template
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 7, 2022Mar 7, 2022

    • LabProtocols

      Public
      Documenting protocols used in the lab. (These are all computational!)
      CSS
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

    • visual-popgen

      Public
      Jupyter book of course notes related to population genetics.
      TeX
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•7•3•0•Updated Dec 22, 2021Dec 22, 2021

    • ComputerSkills4GradStudents

      Public
      "Text book" for Advanced Bioinformatics class at UCI
      TeX
      •0•3•1•0•Updated Sep 19, 2021Sep 19, 2021

    • AdvancedInformatics2021

      Public
      Course materials for 2021
      HTML
      •9•3•1•0•Updated Feb 4, 2021Feb 4, 2021

    • RMarkdown_remark_slides_template

      Public template
      Template repository for "remark" slides generated via R Markdown
      Makefile
      •
      MIT License
      •0•0•0•1•Updated Oct 8, 2020Oct 8, 2020

    • RMarkdown_beamer_slides_template

      Public template
      Template repository for LaTeX "beamer" slides generated in R Markdown
      TeX
      •
      MIT License
      •1•1•0•0•Updated Oct 1, 2020Oct 1, 2020

    • tutorials

      Public
      Light tutorials on coding techniques
      Python
      •0•1•0•0•Updated Mar 6, 2019Mar 6, 2019

    • EE283Winter2019

      Public
      Materials for EE283, winter 2019
      HTML
      •3•0•0•0•Updated Feb 6, 2019Feb 6, 2019

    • AdvInformatics2019Assignment1

      Public
      Assignment 1
      16•0•0•0•Updated Jan 10, 2019Jan 10, 2019

    • hpc_python

      Public
      Tips on compiling python stuff using the lab's module/anaconda hybrid
      0•0•0•0•Updated Nov 14, 2018Nov 14, 2018

    • intro2github

      Public
      Quick intro to github. Contents for UCI journal club on the topic
      1•0•0•0•Updated Oct 12, 2018Oct 12, 2018

    • cuda_installation_ubuntu

      Public
      How we got CUDA installed and Tensor Flow working with GPU
      0•2•0•0•Updated Aug 27, 2018Aug 27, 2018

    • diploshic_sim_example

      Public
      Example using simulated data.
      Shell
      •0•1•0•0•Updated Aug 26, 2018Aug 26, 2018

    • DGRPmasked

      Public
      IBD regions identified in DGRP lines by Cridland et al. (2013) doi: 10.1093/molbev/mst129
      0•0•0•0•Updated Apr 3, 2018Apr 3, 2018

    • fwdpy11_arg_example

      Public
      Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.
      Python
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Mar 21, 2018Mar 21, 2018

    • ESMtest

      Public
      A PLINK-based implementation of the "ESM" test from Thornton, Foran and Long (2013)
      Shell
      •1•1•0•0•Updated Jun 14, 2017Jun 14, 2017

    • Burger2000

      Public
      Notes for reading group on Burger's 2000 book.
      HTML
      •0•0•0•0•Updated Apr 25, 2017Apr 25, 2017

    • AdvancedInformatics2017

      Public
      Materials for EE283
      HTML
      •0•1•0•0•Updated Feb 6, 2017Feb 6, 2017

    • ThorntonLabToolkit

      Public
      Various scripts, etc., for helping write papers.
      Shell
      •0•0•0•0•Updated Aug 18, 2016Aug 18, 2016

    • disease_sims

      Public
      Shell
      •0•0•0•0•Updated Jun 23, 2016Jun 23, 2016

    • getsimyak

      Public
      Shell scripts to download raw data for simulans and yakuba resequencing
      Shell
      •0•0•0•0•Updated Apr 29, 2016Apr 29, 2016

    • DrosophilaPopGenData-Rogers2015

      Public
      Population Genomic Data and SNPs for Drosophila yakuba and Drosophila simulans
      0•0•0•0•Updated Jun 17, 2015Jun 17, 2015

    • TFL2013sim

      Public
      Simulation code from Thornton, Foran and Long (2013) PloS Genetics
      C++
      •0•0•0•0•Updated Jan 2, 2015Jan 2, 2015

    • annotation_methods

      Public
      Methods for genome annotation using paired-end RNA-seq data
      Shell
      •1•1•0•0•Updated Oct 16, 2014Oct 16, 2014

    • Cridland2013pipeline

      Public
      TE presence/absence calling pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129
      C++
      •
      Other
      •0•1•0•0•Updated Oct 8, 2014Oct 8, 2014

    • Cridland2013AnnotPipeline

      Public
      TE annotation pipeline from Cridland et al. (2013) doi: 10.1093/molbev/mst129
      Perl
      •0•1•0•0•Updated Oct 8, 2014Oct 8, 2014