molpopgen
Faculty member in Ecology & Evolutionary Biology at UC Irvine. @ThorntonLab is our group's GitHub account.
University of California IrvineIrvine, CA
Pinned Repositories
BigDataFormats
Tutorial on programming or "big data"/bioinformatics
fwdpp
fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations
fwdpy
forward-time population genetic simulation in python
fwdpy11
Forward-time simulation in Python using fwdpp
gimp_scripts
Plugins for GIMP
libsequence
libsequence: a C++ class library for evolutionary genetic analysis
msstats
msstats calculates many common popgen summary statistics from the output of the coalescent simulation "ms".
pecnv
C++ tools for calling structural variants from PE mapping of short reads.
molpopgen's Repositories
molpopgen/fwdpy11
Forward-time simulation in Python using fwdpp
molpopgen/fwdpp
fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations
molpopgen/text2qti_example
text2qti_example
molpopgen/ancestry-recording-experiments
molpopgen/ancestry_graph
(Yet another) prototype of a new method for ancestry update
molpopgen/backpacking_food
DIY meals for backpacking
molpopgen/demes-rs
rust tools for the demes ecosystem
molpopgen/dod_experiments
Rust DOD experiments
molpopgen/dotfiles
Config files for various programs.
molpopgen/dynamic-ts
Dynamic tree sequences for forward simulations
molpopgen/edge_buffering_explanation
Pure Python description of efficient edge buffering
molpopgen/efficient_edge_recording
Example of efficient edge recording in forward simulation
molpopgen/fedora_notes
Notes on Fedora Linux setup
molpopgen/fwdpy11_infinitesimal
molpopgen/fwdpy11_statistical_tests
Suite of statistical tests for fwdpy11.
molpopgen/genetics_class_material
Material for the in-class portions of genetics (bio 97) at UCI.
molpopgen/jupyter_slides_for_courses
Course slides in Jupyter notebook format
molpopgen/list_container
Designing a container to hold many linked lists and use Vec to back the memory.
molpopgen/moments
molpopgen/msprime_remark_examples
examples of using msprime to provide slide content via pyodide
molpopgen/OpenCL-AMD-Fedora
AMD OpenCL userspace drivers for Fedora.
molpopgen/pybind11_with_static_archive
Experimenting with separating back end from pybind11 modules
molpopgen/pyo3learning
pyO3learning
molpopgen/remark_class_slides
Slides for UCI classes using remarkjs
molpopgen/rexams_test
Example of using the R exams pacakge
molpopgen/rust_scripting_experiments
rust_scripting_experiments
molpopgen/tskit
tskit provides a C and Python API for accessing, analysing and creating tree sequences - a highly efficient way of storing a set of related DNA sequences.
molpopgen/tskit_dev_envs
Docker environments for tskit development
molpopgen/tskit_parallel_presentation
Slides for tskit-dev presentation
molpopgen/unique_item_benchmarks
Benchmarking methods of tracking unique integers (rust)