Software
DEBIAS-M
(Domain adaptation with phenotype Estimation and Batch Integration Across Studies of the Microbiome).
Interpretable inference and correction of processing bias across microbiome batches and studies.
Austin et al., bioRxiv 2024
RebalancedCV
Cross validation while accounting for distributional bias.
Austin et al., arXiv 2024
SCRuB
(Source-tracking for Contamination Removal in microBiomes).
In silico removal of contamination from (microbial) counts data using process controls.
Austin et al., Nature Biotechnology 2023
pymgpipe
A python implementation of mgpipe (Baldini et al., Bioinformatics 2019).
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Meydan et al., JOSS 2023
SGVFinder2
Detection of structural variants in microbial genomes using metagenomic data.
An updated and maintained version of SGVFinder (Zeevi et al., Nature 2019)
CoPTR
Efficient and accurate inference of microbial growth rates from metagenomic data.
SVFinder
Detection of structural variants in microbial genomes using metagenomic data.