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    28 repositories

    • 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 Oct 3, 2024Oct 3, 2024

    • CATE

      Public
      A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
      genomegeneticsanacondacudacondavcfcuda-toolkitvcf-datavcf-files1000genomes
      Cuda
      •
      MIT License
      •0•11•0•0•Updated Oct 3, 2024Oct 3, 2024

    • Transfer-Learning

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 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

    • transTF-TWAS

      Public
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Aug 28, 2024Aug 28, 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
      •0•5•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-sequencingcancer-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.
      transmissionphylogeneticsbayesianinfectious-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