microbiome R package
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
A MALDI Mass Spectrometry Bioinformatics Platform
A comprehensive and customizable R package for microbiome analysis.
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.
SCORE - a consensus tool for detecting differentially expressed genes in bacteria
R package to perform data pre-processing for more informative bacterial GWAS
Microbiome Amplicon Analysis and Visualization
MicroRaman is an R package to process microbial Raman Spectroscopy data
Machine learning classification pipe-line used for the study "Long-term life history predicts current elderly gut microbiome"
An R package to help you PLAying with your genomic DAta.
Automatic classification of bacterial species using Gram-stained images
Methods and data to reproduce the investigation on the adaptive trait found in the genes of the methane oxidation metabolic module of type Ia methanotrophs
Microbial fitness inference from barcode counts.
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
Code for the Lancet Digital Health manuscript
A user-friendly interface for the bioinactivation package
MetaGEN - an all-in-one solution for streamlined metagenomic analyses
Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.
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