Stars
A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.
Lecture Notes on Computational and Mathematical Population Genetics
ABC random forests for model choice and parameter estimation, pure C++ implementation
Drawing functions for Demes demographic models
Removes large or troublesome blobs like git-filter-branch does, but faster. And written in Scala
A set of functions to visualise genotypes based on a VCF
A set of tutorials for msprime and tskit.
A library of standard population genetic models
FastAPI framework, high performance, easy to learn, fast to code, ready for production
STAT 453: Intro to Deep Learning @ UW-Madison (Spring 2020)
An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.
sci-f / snakemake.scif
Forked from fbartusch/snakemake_tutorialTutorial with snakemake and Scientific Filesystem
Machine Learning Experiments and Work
A cookiecutter template for Snakemake workflows
A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.
A repo holding my poster displayed at SMBE2019, with some extra information.
Docker image for the SMBE speciation genomics workshop
An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
This is the starting code for endcoding an msprime TreeSequence Object into a 3D array for ML and visualization purposes
Sets up an autoscaled Jetstream cluster for SRA work
Command-line tool to manage bibliography (pdfs + bibtex)
Multi-Scale Context Aggregation by Dilated Convolutions in Keras.
High-level tools to simplify visualization in Python.