PoonLab

Pinned Repositories

bayroot
Bayesian root-to-tip regression for dating reservoir sequences
Language:R53
clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
Language:R00
covizu
Rapid analysis and visualization of coronavirus genome variation
Language:JavaScript45 6 42720
gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
Language:Python3 5 912
HexSE
Simulation of molecular evolution with overlapping reading frames
Language:Python42
Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
Language:R4 6 1462
MiCall-Lite
Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
Language:Python4 5 403
sam2conseq
Language:Python6 6 170
sierra-local
Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
Language:Python6 8 913
twt
Generic framework for the coalescent simulation of pathogen trees within host trees in R
Language:R3 6 1402

PoonLab's Repositories

PoonLab/covizu
Rapid analysis and visualization of coronavirus genome variation
Language:JavaScript45 6 42720
PoonLab/sam2conseq
Language:Python6 6 170
PoonLab/sierra-local
Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
Language:Python6 8 913
PoonLab/bayroot
Bayesian root-to-tip regression for dating reservoir sequences
Language:R53
PoonLab/HexSE
Simulation of molecular evolution with overlapping reading frames
Language:Python42
PoonLab/Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
Language:R4 6 1462
PoonLab/MiCall-Lite
Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
Language:Python4 5 403
PoonLab/gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
Language:Python3 5 912
PoonLab/twt
Generic framework for the coalescent simulation of pathogen trees within host trees in R
Language:R3 6 1402
PoonLab/courses
Language:Python2 3 815
PoonLab/fluclades
Genetic taxonomy of influenza A virus subtypes
Language:Python2
PoonLab/ovrf-viz
Review article on overlapping reading frames in viruses
Language:Python20
PoonLab/plodex
Interactive visualization of SARS-CoV-2 variants
Language:Python2 4 6
PoonLab/clmp
Genetic clustering with Markov-modulated Poisson processes
Language:C12
PoonLab/cophylo
Data and scripts associated with manuscript on Tree Metrics of Cophylogeny
Language:R1 3 12
PoonLab/highlineR
An implementation of LANL's Highlighter web app in R for batch processing and scaling
Language:R12
PoonLab/vindels
Developing an empirical model of sequence insertion and deletion in virus genomes
Language:R1 3 103
PoonLab/clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
Language:R00
PoonLab/indelrates
Data and scripts used for HIV-1 group M indel rate estimation project
Language:Python01
PoonLab/Poplars
Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database
Language:Shell00
PoonLab/Bioplus
In-house scripts that extend the functionality of Biopython
Language:Python
PoonLab/comet-prot
Book chapter for upcoming Springer book Computational Methods in Protein Evolution
Language:HyPhy2
PoonLab/constellations
Language:Python
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
Language:C++
PoonLab/KaphiShiny
A Shiny web interface for running Kaphi
Language:R
PoonLab/sup
Sequencing Uncertainty Propagation
Language:R
PoonLab/test
Language:Python
PoonLab/tn
Optimization of genetic clustering methods by predictive modeling
Language:R
PoonLab/tragula
Mapping networks of shared research expertise by word embedding analysis
Language:Python
PoonLab/tuning-disorder-virus
Ensemble classifier of intrinsic protein disorder for viruses
Language:Python