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mia:Microbiome analysis
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
Maintained by Tuomas Borman. Last updated 18 hours ago.
microbiomesoftwaredataimportanalysisbioconductorcpp
51 stars 11.52 score 316 scripts 5 dependentsbioc
decontam:Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.
Maintained by Benjamin Callahan. Last updated 5 months ago.
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioinformaticscontaminationmetabarcoding
153 stars 11.42 score 524 scripts 6 dependents