signatureSearch

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 (3.11)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script signatureSearch
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software
Version 1.1.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray
LinkingTo Rcpp
Suggests knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db
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_1.1.1.tar.gz
Windows Binary signatureSearch_1.1.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) signatureSearch_1.1.1.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

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