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.
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Updated
May 28, 2022 - 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 taxonomy construction and evaluation in R
Bacterial Epigenomics Analysis SuiTe
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.
Groundwater flow and microbes transport modelling with R and Modflow / Modpath
Simulate pangenomes according to the IMG + Neutral models
Predicts bacterial resistome
Finding Tn-Seq Essential genes (FiTnEss)
AU microbiome molecular exploratory analyses for NSW
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
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).
R-Scripts and Fiji-macro used for the construction of kymographs based on fluorescence profiles
MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.
Full genome of E. coli, strain K12 MG1655
Annotation for full-genome assembly of Escherichia coli str. K12, substr. MG1655
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