DOI: 10.18129/B9.bioc.signatureSearch    

This is the development version of signatureSearch; for the stable release version, see signatureSearch.

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Bioconductor version: Development (3.15)

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 [cre, aut], Thomas Girke [aut]

Maintainer: Yuzhu Duan <yduan004 at>

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


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biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version 1.9.1
In Bioconductor since BioC 3.10 (R-3.6) (2 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, tools
LinkingTo Rcpp
Suggests knitr, testthat, rmarkdown, BiocStyle,, signatureSearchData, DT
SystemRequirements C++11
Depends On Me
Imports Me signatureSearchData
Suggests Me
Links To Me
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Source Package signatureSearch_1.9.1.tar.gz
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