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bioc
lefser:R implementation of the LEfSE method for microbiome biomarker discovery
lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).
Maintained by Sehyun Oh. Last updated 1 months ago.
softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-packager01ca230551
11.0 match 56 stars 8.44 score 56 scripts
waldronlab
MicrobiomeBenchmarkData:Datasets for benchmarking in microbiome research
The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.
Maintained by Samuel Gamboa. Last updated 5 months ago.
experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-packager01ca230551
11.0 match 4.39 score 18 scripts