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Here are some of my past and ongoing projects, which I think are pretty cool. Not all projects are being actively developed, but I will certainly respond to issues and pull requests.

I am the main developer for (more recent projects are listed first):

  • GhostKnockoffGWAS: Package for performing knockoff-based analysis for GWAS summary statistics data
  • Ghostbasil.jl: (WIP) Provides Julia wrappers to the C++ code of ghostbasil
  • Knockoffs.jl: Implements the knockoff filter framework for variable selection, which performs conditional independence testing and controls the FDR (false discovery rate)
  • groupknockoffs: Simple app to solve group knockoff optimization, without Julia installed!
  • EasyLD.jl: Julia utilities for downloading and reading LD (linkage disequilibrium) matrices stored in Hail's BlockMatrix format
  • knockoffspy: A Python package that provides a direct wrapper over Knockoffs.jl
  • knockoffsr: A R package that provides a direct wrapper over Knockoffs.jl
  • MendelIHT.jl: Implements iterative hard thresholding (l0 penalized regression solver). It is highly optimized for handling compressed (binary PLINK) genotype data
  • MendelImpute.jl: A package for genotype imputation, phasing, and (global/local) ancestry inference utilizing a reference haplotype panel. It is significantly faster than existing methods but slightly less accurate
  • Thyrosim.jl: An updated version of THYROSIM, Thyrosim.jl produces individualized thyroid hormone predictions (TT4/TT3/TSH) based on a rather complicated ODE model
  • VCFTools.jl: Julia utilities for handling VCF (Variant Call Format) files
  • fastPHASE.jl: Julia wrapper for the famous fastPHASE genetics software. The primary use case is to allow the original program to run on binary PLINK data.

I am a contributor for (at least 5 commits):

  • QuasiCopula.jl: Implements a new class of distribution (Quasi-Copulas) that captures correlation among non-Gaussian random variables efficiently
  • SnpArrays.jl: Julia package for handling binary PLINK formatted data. It has the fastest (matrix)-(vector) multiplication routine for compressed PLINK files as far as I know.
  • MendelKinship.jl: Calculates various empirical and theoretical kinship coefficients, based on pedigree or genotype data.

Benjamin Chu's Projects

diffeqparamestim.jl icon diffeqparamestim.jl

Easy scientific machine learning (SciML) parameter estimation with pre-built loss functions

fastphase.jl icon fastphase.jl

Julia wrapper for the fastPHASE genetics software (this is WIP)

glmnet.jl icon glmnet.jl

Julia wrapper for fitting Lasso/ElasticNet GLM models using glmnet

groupknockoff icon groupknockoff

Building a simple executable for solving group knockoff optimization

hdf5.jl icon hdf5.jl

Save and load data in the HDF5 file format from Julia

hoffman2tutorials icon hoffman2tutorials

Tutorials for UCLA's Hoffman2 HPC Cluster Computing Resource for R and Julia

julia.jl icon julia.jl

Curated decibans of Julia programming language.

mendelaimselection.jl icon mendelaimselection.jl

This analysis option selects the SNPs that are most informative at predicting ancestry for your data — the best Ancestry Informative Markers (AIMs).

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