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Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Bioconductor version: Release (3.19)

This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.

Author: Yuzhu Duan [aut], Brendan Gongol [cre, aut], Thomas Girke [aut]

Maintainer: Brendan Gongol <bgong001 at>

Citation (from within R, enter citation("signatureSearch")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

signatureSearch HTML R Script
Reference Manual PDF


biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), Rcpp, SummarizedExperiment,
Imports AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble
System Requirements C++11
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Suggests knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT
Linking To Rcpp
Depends On Me
Imports Me DFD
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Follow Installation instructions to use this package in your R session.

Source Package signatureSearch_1.18.0.tar.gz
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macOS Binary (x86_64) signatureSearch_1.18.0.tgz
macOS Binary (arm64) signatureSearch_1.18.0.tgz
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Source Repository (Developer Access) git clone
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