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).
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softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-packager01ca230551
8.67 score 68 stars 115 scripts 1.5k downloadsGenomicSuperSignature - Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.
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transcriptomicssystemsbiologyprincipalcomponentrnaseqsequencingpathwaysclusteringbioconductor-packageexploratory-data-analysisgseameshprincipal-component-analysisrna-sequencing-profilestransferlearningu24ca289073
7.28 score 16 stars 66 scripts 501 downloadsAnVILWorkflow - Run workflows implemented in Terra/AnVIL workspace
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.
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infrastructuresoftwareanvilgcpterrau24hg010263workflows
5.72 score 7 stars 7 scripts 247 downloads