Nardus Mollentze's repositories
zoonotic_rank
Code and data used in Mollentze et al. (2021) "Identifying and prioritizing potential human-infecting viruses from their genome sequences".
beast_utils
A python library for generating and manipulating BEAST 1 XML files
isg_composition
Code for the machine learning component of Shaw, Rihn, Mollentze, et al. (2021) "The ‘antiviral state’ has shaped the CpG composition of the vertebrate interferome".
borrelia_workflow
Borrelia mapping and variant calling snakemake pipeline
covid-uk
A fork of LSHTM's COVID-19 model to adapt to our data
geo_features
A python library for calculating geographical summary statistics
hiv_growth_rates
Code used in Sugrue et al. (2021), "The interferon resistance of transmitted HIV-1 is a consequence of enhanced replicative fitness".
SCRCdataAPI
Package for hdf5 processing in R
stnn
Packaged version of Delasalles et al.'s spatio-temporal neural network model