Sarah Nadeau's repositories
cov-europe-bdmm
Code for the publication "The origin and early spread of SARS-CoV-2 in Europe"
burk-nextstrain
An automated nextstrain build for Burkholderia pseudomallei
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
bioinf-containers
This repository has code to build containers for bioinformatics tools.
bioinf-workflows
This repository has bioinformatics workflows written with Nextflow.
cov-swiss-phylo
Code for the manuscript "Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data".
data_analysis_course
This repository hosts materials for the Data Analysis course hosted by IOB Scientific Computing.
great-style
A CSS to make your page look great.
IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Reassortment-Tutorial
Tutorial for the coalescent with reassortment
sarah-portfolio
An example of my coding work.
single_cell_utils
Utility scripts for working with single-cell RNA seq data
swga-coxiella
This repository records efforts to reproduce the results of Cocking et al.'s SWGA for Coxiella burnetii.
swga-lepto
This repository is to record efforts at primer design for selective whole-genome amplification for pathogenic Leptospira.
tree-pruner
Get a small, representative genome set from a large phylogenetic tree.
treetime_examples
A collection of documented examples using TreeTime