signatureSearch

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Bioconductor version: 3.23 · Package version: 1.26.0

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

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("signatureSearch")

Details

Maintainer	Brendan Gongol <bgong001@ucr.edu>
Author	Yuzhu Duan [aut], Brendan Gongol [cre, aut], Thomas Girke [aut]
License	Artistic-2.0
URL	https://github.com/yduan004/signatureSearch/
Bug Reports	https://github.com/yduan004/signatureSearch/issues
System Requirements	C++20
Downloads rank	422
Source branch	RELEASE_3_23
biocViews	Coverage, DifferentialExpression, GO, GeneExpression, NetworkEnrichment, Sequencing, Software

Documentation

signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Download

Source package

Dependencies

Depends: R (>= 4.5.0), Rcpp, SummarizedExperiment, org.Hs.eg.db

Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, readr, rhdf5, GSEABase, DelayedArray, GO.db, BiocGenerics, tibble, DOSE, AnnotationHub, stringr

LinkingTo: Rcpp

Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT

Reverse dependencies

Suggests Me (1): DFD