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).

Last updated 25 days ago

softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package

8.35 score 43 stars 59 scripts 863 downloads

GenomicSuperSignature - 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.

Last updated 27 days ago

transcriptomicssystemsbiologyprincipalcomponentrnaseqsequencingpathwaysclusteringbioconductor-packageexploratory-data-analysisgseameshprincipal-component-analysisrna-sequencing-profilestransferlearning

6.97 score 16 stars 59 scripts 192 downloads

AnVILWorkflow - 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.

Last updated 27 days ago

infrastructuresoftwareanvilgcpterraworkflows

5.88 score 5 stars 1 scripts 112 downloads

OmicsMLRepoR - Search harmonized metadata created under the OmicsMLRepo project

This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.

Last updated 27 days ago

softwareinfrastructuredatarepresentation

5.02 score 9 scripts