Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi

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

Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/

Workflow for the processsing of data from the DCV evolutionary experiments.

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

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

This repo contains applications of the tool VILOCA.

Map single-cell transcriptomes to copy number evolutionary trees.