signatureSearch

This is the released version of signatureSearch; for the devel version, see signatureSearch.

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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DOI: 10.18129/B9.bioc.signatureSearch

Bioconductor version: Release (3.22)

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 "4.5") and enter:


if (!require("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")

signatureSearch HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

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

Linking To Rcpp

Enhances

Depends On Me DFD

Imports Me

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_1.24.0.tar.gz

Windows Binary (x86_64) signatureSearch_1.24.0.zip (64-bit only)

macOS Binary (x86_64) signatureSearch_1.24.0.tgz

macOS Binary (arm64) signatureSearch_1.24.0.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/

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