Fitness estimates of SARS-CoV-2 variants

Probabilistic modeling of high-dimensional binary data in JAX

Wrangling short-read sequencing data for import into SILO

FiTree: Bayesian inference of fitness landscapes via tree-structured branching processes

BSSE COVID-19 sequencing of test swab samples

Personalised mutual hazard networks: fixed effects in cancer progression modeling

Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem

VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data

smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.

Wastewater-derived Respiratory Syncytial Virus data analysis