SarahNadeau

Grapevine-SARS-CoV-2-Introduction-Analysis

Pipeline for estimating putatively independent introductions of SARS-CoV-2 from genome sequences.

harvester-database-and-automation

The database and automation infrastructure used in the Swiss SARS-CoV-2 Sequencing Consortium (S3C)

POUMM-GWAS

Scripts for "A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits".

aarhus-datathon-genome-study-1

burk-nextstrain

An automated nextstrain build for Burkholderia pseudomallei

cluster-detection

cov-europe-bdmm

Code for the publication "The origin and early spread of SARS-CoV-2 in Europe"

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

triplet-taxonomy-classification

wf-swga

This project houses a Nextflow workflow to propose primers for selective whole-genome amplification.

SarahNadeau/cov-europe-bdmm

Code for the publication "The origin and early spread of SARS-CoV-2 in Europe"

SarahNadeau/wf-swga

This project houses a Nextflow workflow to propose primers for selective whole-genome amplification.

SarahNadeau/burk-nextstrain

An automated nextstrain build for Burkholderia pseudomallei

SarahNadeau/cluster-detection

SarahNadeau/docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

SarahNadeau/triplet-taxonomy-classification

SarahNadeau/aarhus-datathon-genome-study-1

SarahNadeau/bioinf-containers

This repository has code to build containers for bioinformatics tools.

SarahNadeau/bioinf-workflows

This repository has bioinformatics workflows written with Nextflow.

SarahNadeau/cov-swiss-phylo

Code for the manuscript "Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data".

SarahNadeau/data_analysis_course

This repository hosts materials for the Data Analysis course hosted by IOB Scientific Computing.

SarahNadeau/datascience-projectB

SarahNadeau/docker-playground

SarahNadeau/estimateR

R package for deconvolution & estimation of effective R_e of Covid-19

SarahNadeau/great-style

A CSS to make your page look great.

SarahNadeau/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

SarahNadeau/k-mer-taxonomy-classification

SarahNadeau/knn-taxonomy-classification

SarahNadeau/Reassortment-Tutorial

Tutorial for the coalescent with reassortment

SarahNadeau/sarah-portfolio

An example of my coding work.

SarahNadeau/sib-variant-analysis

SarahNadeau/single_cell_utils

Utility scripts for working with single-cell RNA seq data

SarahNadeau/snptree

Generate a core genome alignment, call SNPs, and make a tree based on bacterial genome assemblies.

SarahNadeau/swga-coxiella

This repository records efforts to reproduce the results of Cocking et al.'s SWGA for Coxiella burnetii.

SarahNadeau/swga-lepto

This repository is to record efforts at primer design for selective whole-genome amplification for pathogenic Leptospira.

SarahNadeau/tree-pruner

Get a small, representative genome set from a large phylogenetic tree.

SarahNadeau/treetime_examples

A collection of documented examples using TreeTime

SarahNadeau/wf-assembly-snps