DOI: 10.18129/B9.bioc.signatureSearch  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see signatureSearch.

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Bioconductor version: 3.16

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")):


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biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License Artistic-2.0
Depends R (>= 3.6.0), 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
LinkingTo Rcpp
Suggests knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
Links To Me
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