venkataduvvuri

phylosamp

The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.

adapref

R package to do adaptive preferential sampling in phylodynamics

AMR_prediction

A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains.

aiSource

Repository for the paper "Machine learning to predict the source of campylobacteriosis using whole genome data"

causallib

A Python package for modular causal inference analysis and model evaluations

cchsflow

Variable transformation and harmonization for the Canadian Community Health Survey

cov2clusters

Stable clustering of SARS-CoV-2 sequences from phylogenetic trees

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dna-pytorch-tutorial

a super basic tutorial on how to create a pytorch models for raw DNA sequences

EpiCoV_downloader

Download all EpiCoV sequcnes from GISAID

EVEscape

Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"

google-research

Google Research - TabNet

HAWK

Hitting associations with k-mers

In-BoXBART

In-BoXBART: Get Instructions into Biomedical Multi-task Learning

lr2cluster

[Package] Cluster Assignment Using Multiple Sources of Data

nf-flu

Influenza genome analysis Nextflow workflow

opqua

Epidemiological modeling framework for pathogen population genetics and evolution.

ORC

Optimised relaxed clock (ORC)

outbreaker2

Disease outbreak reconstruction from epidemiological and genetic data

Phylodynamic-Subsampling

pipeline-resources

Bioinformatics Pipeline and Visualization resources

Sabres

A tool that scans VCF data for SARS-CoV-2 Antiviral Resistance

shusher

Private, browser-based placement of genome sequences on phylogenetic trees using UShER.

Simplot_PlusPlus

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

StrainHub

Welcome to the StrainHub Repo - Files and Data - StrainHub Online:

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

usher

Ultrafast Sample Placement on Existing Trees

weathercan

R package for downloading weather data from Environment and Climate Change Canada