Repositories list

• Apollo

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

  Cuda

  •

  MIT License

  •0•1•0•0•Updated Nov 23, 2024Nov 23, 2024

• Transfer-Learning

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• CATE

  Public
  A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

  genomegeneticsanaconda+ 15cudacondavcfepidemiologyhivviral-genomics1000genomes+ 8

  Cuda

  •

  MIT License

  •0•11•0•0•Updated Oct 26, 2024Oct 26, 2024

• transTF-TWAS

  Public
  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Oct 17, 2024Oct 17, 2024

• AE-TWAS

  Public
  Python

  •0•3•0•0•Updated Sep 19, 2024Sep 19, 2024

• Jawamix5

  Public
  Java

  •1•4•0•1•Updated Sep 17, 2024Sep 17, 2024

• 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, followed by a kernel- based density estimation (KDE).

  R

  •

  MIT License

  •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

• TF-TWAS

  Public
  R

  •

  GNU General Public License v3.0

  •1•6•1•0•Updated Oct 13, 2023Oct 13, 2023

• IMAS

  Public
  R

  •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

• Proteomics

  Public
  MIT License

  •0•0•0•0•Updated Sep 14, 2023Sep 14, 2023

• Grad-Learn

  Public
  Python

  •0•0•0•0•Updated Aug 14, 2023Aug 14, 2023

• CVc_in_bioinformatics

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Aug 1, 2023Aug 1, 2023

• PRESM

  Public
  Personalized reference editor for somatic mutation discovery

  bioinformaticssomatic-variantsnext-generation-sequencing+ 3cancer-genomicssomatic-mutationspresm

  Java

  •

  MIT License

  •0•0•0•1•Updated Dec 2, 2022Dec 2, 2022

• Withinhost_evolution_Transmission

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

  Slim

  •0•0•0•0•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 using SARS-CoV-2 genomic sequences. Our pipeline is built upon the BEAST2 and TransPhylo software.

  transmissionphylogeneticsbayesian+ 5infectious-diseasesbeast2covid19covid19-trackertransphylo

  R

  •

  MIT License

  •0•4•0•0•Updated Dec 16, 2021Dec 16, 2021

• seqmodel

  Public
  Genomic representation learning framework

  Python

  •0•1•0•0•Updated Mar 29, 2021Mar 29, 2021

• PoolHapDev

  Public
  Java

  •0•0•1•0•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 tree to predict novel transmission clusters as well as Infection dates of patients using Sanger seqeuncing data.

  R

  •0•3•0•0•Updated Dec 23, 2020Dec 23, 2020

• PoolHapX

  Public
  PoolHapX

  Java

  •1•5•4•0•Updated Dec 7, 2020Dec 7, 2020

• mkTWAS

  Public
  mkTWAS

  Java

  •0•0•1•0•Updated Nov 14, 2020Nov 14, 2020

• FIGS

  Public
  FIGS

  0•0•0•0•Updated Nov 14, 2020Nov 14, 2020

• WgLink

  Public
  Java

  •1•0•0•0•Updated Aug 16, 2020Aug 16, 2020

• kTWAS

  Public
  Java

  •2•5•0•0•Updated Jul 2, 2020Jul 2, 2020

• phx-nn

  Public
  PoolHapX parameter tuning neural network

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2020Feb 26, 2020

• phx-parameter-map

  Public
  Mapping PoolHapX parameter sets to performance metrics.

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2020Feb 26, 2020

• OCMA

  Public
  OCMA: Out-of-Core Matrices Analyzer

  0•1•0•0•Updated Dec 25, 2019Dec 25, 2019

• PoolHapX-old

  Public archive
  Java

  •

  MIT License

  •0•1•0•0•Updated May 27, 2019May 27, 2019

• group-lasso-nn

  Public archive
  Deep Learning implementations for the group lasso project.

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 4, 2019Apr 4, 2019