signatureSearch

DOI: 10.18129/B9.bioc.signatureSearch    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see signatureSearch.

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Bioconductor version: 3.13

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 ucr.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("signatureSearch")

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

Documentation

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

browseVignettes("signatureSearch")

 

HTML	R Script	signatureSearch
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version	1.6.3
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
LinkingTo	Rcpp
Suggests	knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db, signatureSearchData, DT
SystemRequirements	C++11
Enhances
URL	https://github.com/yduan004/signatureSearch/
BugReports	https://github.com/yduan004/signatureSearch/issues
Depends On Me
Imports Me	signatureSearchData
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	signatureSearch_1.6.3.tar.gz
Windows Binary	signatureSearch_1.6.3.zip
macOS 10.13 (High Sierra)	signatureSearch_1.6.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/signatureSearch
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/signatureSearch
Package Short Url	https://bioconductor.org/packages/signatureSearch/
Package Downloads Report	Download Stats