Repositories list

• CATE

  Public
  A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/1…

  genomegeneticsanaconda+ 15

  genomegeneticsanacondacudacondavcfepidemiologyhivviral-genomics1000genomes+ 8

  Cuda

  •

  MIT License

  •00 forks•1515 stars•00 issues•00 pull requests•Updated Apr 12, 2026Apr 12, 2026

• Transfer-Learning

  Public
  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• moka

  Public
  MOKA Snakemake pipeline for GWAS incorporating user provided multi-omics data sources such as gene expression, neural network weights, transcription factor bind…

  R

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2025Oct 8, 2025

• Kernel_smoothed_permutation

  Public
  Kernel-smoothed permutation is a method that constructs the null distribution of a test statistic through a novel kurtosis-driven Box-Cox transformation, follow…

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 16, 2025Sep 16, 2025

• Apollo

  Public
  A comprehensive simulator for exploring the dynamics of viral transmission complete with within host evolution.

  Cuda

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 17, 2025Jun 17, 2025

• AE-TWAS

  Public
  Python

  •11 fork•33 stars•11 issue•00 pull requests•Updated Mar 25, 2025Mar 25, 2025

• transTF-TWAS

  Public
  Python

  •

  GNU General Public License v3.0

  •11 fork•55 stars•00 issues•00 pull requests•Updated Oct 17, 2024Oct 17, 2024

• Jawamix5

  Public
  Java

  •11 fork•44 stars•00 issues•11 pull request•Updated Sep 17, 2024Sep 17, 2024

• TF-TWAS

  Public
  R

  •

  GNU General Public License v3.0

  •11 fork•66 stars•11 issue•00 pull requests•Updated Oct 13, 2023Oct 13, 2023

• IMAS

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 15, 2023Sep 15, 2023

• Proteomics

  Public
  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 14, 2023Sep 14, 2023

• Grad-Learn

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 14, 2023Aug 14, 2023

• CVc_in_bioinformatics

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 1, 2023Aug 1, 2023

• PRESM

  Public
  Personalized reference editor for somatic mutation discovery

  bioinformaticssomatic-variantsnext-generation-sequencing+ 3

  bioinformaticssomatic-variantsnext-generation-sequencingcancer-genomicssomatic-mutationspresm

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•11 pull request•Updated Dec 2, 2022Dec 2, 2022

• Withinhost_evolution_Transmission

  Public
  Scripts and Code for the simulation of within host dynamics with host transmissions

  Slim

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2022Jun 18, 2022

• TransCOVID

  Public
  A dedicated pipeline designed for the inference of COVID19 transmission networks in a population complete with the prediction of unsampled sources of infection …

  transmissionphylogeneticsbayesian+ 5

  transmissionphylogeneticsbayesianinfectious-diseasesbeast2covid19covid19-trackertransphylo

  R

  •

  MIT License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Dec 16, 2021Dec 16, 2021

• seqmodel

  Public
  Genomic representation learning framework

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 29, 2021Mar 29, 2021

• PoolHapDev

  Public
  Java

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jan 8, 2021Jan 8, 2021

• Transmission_Analyzer

  Public
  A pipeline that enables the prediction of HIV transmission and Infection date inference. The provided R code can be utilised to analyse a BEAST2 generated MCC t…

  R

  •00 forks•33 stars•00 issues•00 pull requests•Updated Dec 23, 2020Dec 23, 2020

• PoolHapX

  Public
  PoolHapX

  Java

  •11 fork•66 stars•44 issues•00 pull requests•Updated Dec 7, 2020Dec 7, 2020

• mkTWAS

  Public
  mkTWAS

  Java

  •00 forks•00 stars•11 issue•00 pull requests•Updated Nov 14, 2020Nov 14, 2020

• FIGS

  Public
  FIGS

  00 forks•00 stars•00 issues•00 pull requests•Updated Nov 14, 2020Nov 14, 2020

• WgLink

  Public
  Java

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 16, 2020Aug 16, 2020

• kTWAS

  Public
  Java

  •11 fork•66 stars•00 issues•00 pull requests•Updated Jul 2, 2020Jul 2, 2020

• phx-nn

  Public
  PoolHapX parameter tuning neural network

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 26, 2020Feb 26, 2020

• phx-parameter-map

  Public
  Mapping PoolHapX parameter sets to performance metrics.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 26, 2020Feb 26, 2020

• OCMA

  Public
  OCMA: Out-of-Core Matrices Analyzer

  00 forks•11 star•00 issues•00 pull requests•Updated Dec 25, 2019Dec 25, 2019

• PoolHapX-old

  Public archive
  Java

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated May 27, 2019May 27, 2019

• group-lasso-nn

  Public archive
  Deep Learning implementations for the group lasso project.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2019Apr 4, 2019