SarahNadeau

cov-europe-bdmm

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

wf-swga

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

burk-nextstrain

An automated nextstrain build for Burkholderia pseudomallei

cluster-detection

docker-builds

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

triplet-taxonomy-classification

aarhus-datathon-genome-study-1

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.

datascience-projectB

docker-playground

estimateR

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

great-style

A CSS to make your page look great.

IsoQuant

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

k-mer-taxonomy-classification

knn-taxonomy-classification

Reassortment-Tutorial

Tutorial for the coalescent with reassortment

sarah-portfolio

An example of my coding work.

sib-variant-analysis

single_cell_utils

Utility scripts for working with single-cell RNA seq data

snptree

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

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

wf-assembly-snps