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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 (3.19)

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 ucr.edu>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
signatureSearch HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), 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, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble
System Requirements C++11
URL https://github.com/yduan004/signatureSearch/
Bug Reports https://github.com/yduan004/signatureSearch/issues
See More
Suggests knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT
Linking To Rcpp
Enhances
Depends On Me
Imports Me DFD
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package signatureSearch_1.17.0.tar.gz
Windows Binary signatureSearch_1.17.0.zip
macOS Binary (x86_64) signatureSearch_1.17.0.tgz
macOS Binary (arm64) signatureSearch_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/signatureSearch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/signatureSearch
Bioc Package Browser https://code.bioconductor.org/browse/signatureSearch/
Package Short Url https://bioconductor.org/packages/signatureSearch/
Package Downloads Report Download Stats