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Bioconductor - signatureSearch (development version)

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 (3.22)

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")

# 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")
Details biocViews Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 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 Package Archives

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

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