EnrichmentBrowser - Seamless navigation through combined results of set-based and network-based enrichment analysis
The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
Last updated 4 months ago
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting
19 stars 3.52 score 87 dependencies 3 dependentsPathNet - An R package for pathway analysis using topological information
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
Last updated 4 months ago
pathwaysdifferentialexpressionmultiplecomparisonkeggnetworkenrichmentnetwork
2.60 score 0 dependenciessafe - Significance Analysis of Function and Expression
SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.
Last updated 4 months ago
differentialexpressionpathwaysgenesetenrichmentstatisticalmethodsoftware
2.14 score 39 dependencies 5 dependentsGSEABenchmarkeR - Reproducible GSEA Benchmarking
The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.
Last updated 4 months ago
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting
13 stars 2.09 score 102 dependenciesCNVRanger - Summarization and expression/phenotype association of CNV ranges
The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.
Last updated 4 months ago
copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnp
7 stars 1.75 score 64 dependenciesbugsigdbr - R-side access to published microbial signatures from BugSigDB
The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
Last updated 4 months ago
dataimportgenesetenrichmentmetagenomicsmicrobiome
3 stars 1.45 score 46 dependencies