Pinned Repositories
bayroot
Bayesian root-to-tip regression for dating reservoir sequences
clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
covizu
Rapid analysis and visualization of coronavirus genome variation
gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
HexSE
Simulation of molecular evolution with overlapping reading frames
Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
MiCall-Lite
Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
sam2conseq
sierra-local
Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
twt
Generic framework for the coalescent simulation of pathogen trees within host trees in R
PoonLab's Repositories
PoonLab/covizu
Rapid analysis and visualization of coronavirus genome variation
PoonLab/sam2conseq
PoonLab/sierra-local
Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
PoonLab/bayroot
Bayesian root-to-tip regression for dating reservoir sequences
PoonLab/HexSE
Simulation of molecular evolution with overlapping reading frames
PoonLab/Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
PoonLab/MiCall-Lite
Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
PoonLab/gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
PoonLab/twt
Generic framework for the coalescent simulation of pathogen trees within host trees in R
PoonLab/courses
PoonLab/fluclades
Genetic taxonomy of influenza A virus subtypes
PoonLab/ovrf-viz
Review article on overlapping reading frames in viruses
PoonLab/plodex
Interactive visualization of SARS-CoV-2 variants
PoonLab/clmp
Genetic clustering with Markov-modulated Poisson processes
PoonLab/cophylo
Data and scripts associated with manuscript on Tree Metrics of Cophylogeny
PoonLab/highlineR
An implementation of LANL's Highlighter web app in R for batch processing and scaling
PoonLab/vindels
Developing an empirical model of sequence insertion and deletion in virus genomes
PoonLab/clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
PoonLab/indelrates
Data and scripts used for HIV-1 group M indel rate estimation project
PoonLab/Poplars
Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database
PoonLab/Bioplus
In-house scripts that extend the functionality of Biopython
PoonLab/comet-prot
Book chapter for upcoming Springer book Computational Methods in Protein Evolution
PoonLab/constellations
PoonLab/dynsbmR
Fork of read-only mirror of the CRAN R package repository. dynsbm — Dynamic Stochastic Block Models. Homepage: http://lbbe.univ-lyon1.fr/dynsbm
PoonLab/KaphiShiny
A Shiny web interface for running Kaphi
PoonLab/sup
Sequencing Uncertainty Propagation
PoonLab/test
PoonLab/tn
Optimization of genetic clustering methods by predictive modeling
PoonLab/tragula
Mapping networks of shared research expertise by word embedding analysis
PoonLab/tuning-disorder-virus
Ensemble classifier of intrinsic protein disorder for viruses