Bacterial taxonomy construction and evaluation in R

Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.

Bacterial Epigenomics Analysis SuiTe

Simulate pangenomes according to the IMG + Neutral models

Groundwater flow and microbes transport modelling with R and Modflow / Modpath

Code and data for my scientific publications

Predicts bacterial resistome

MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.

Code and Data related to Wimmer and Morais et al (2023)

Ecological and Genomic Characterization of Streamlined, Rhodopsin-bearing Freshwater Microbes

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

Finding Tn-Seq Essential genes (FiTnEss)

Code for https://doi.org/10.1094/pdis-05-20-0945-re

AU microbiome molecular exploratory analyses for NSW

Full genome of E. coli, strain K12 MG1655

Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).

Code used to produce results and figures for BA Pathology project on the prospects of a BCG vaccine program in Great Britain. Developed by Joanna Vieira O'Neill, University of Cambridge.

Full-genome assembly of Pseudomonas aeruginosa, str. PAO1

R-Scripts and Fiji-macro used for the construction of kymographs based on fluorescence profiles