Pinned Repositories
AE-TWAS
CATE
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8
Jawamix5
kTWAS
PoolHapX
PoolHapX
seqmodel
Genomic representation learning framework
TF-TWAS
TransCOVID
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.
Transmission_Analyzer
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.
transTF-TWAS
The Long Lab's Repositories
theLongLab/CATE
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8
theLongLab/kTWAS
theLongLab/PoolHapX
PoolHapX
theLongLab/TF-TWAS
theLongLab/transTF-TWAS
theLongLab/Jawamix5
theLongLab/TransCOVID
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.
theLongLab/AE-TWAS
theLongLab/Transmission_Analyzer
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.
theLongLab/seqmodel
Genomic representation learning framework
theLongLab/Apollo
A comprehensive simulator for exploring the dynamics of viral transmission complete with within host evolution.
theLongLab/OCMA
OCMA: Out-of-Core Matrices Analyzer
theLongLab/PoolHapX-old
theLongLab/FIGS
FIGS
theLongLab/Grad-Learn
theLongLab/mkTWAS
mkTWAS
theLongLab/phx-parameter-map
Mapping PoolHapX parameter sets to performance metrics.
theLongLab/Withinhost_evolution_Transmission
Scripts and Code for the simulation of within host dynamics with host transmissions
theLongLab/CVc_in_bioinformatics
theLongLab/group-lasso-nn
Deep Learning implementations for the group lasso project.
theLongLab/IMAS
theLongLab/Kernel_smoothed_permutation
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).
theLongLab/phx-nn
PoolHapX parameter tuning neural network
theLongLab/PoolHapDev
theLongLab/PRESM
Personalized reference editor for somatic mutation discovery
theLongLab/Proteomics
theLongLab/Transfer-Learning
theLongLab/WgLink