signatureSearch
This is the released version of signatureSearch; for the devel version, see signatureSearch.
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Bioconductor version: Release (3.23)
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("signatureSearch")):Yuzhu Duan, Brendan Gongol, Thomas Girke. signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis. doi:10.18129/B9.bioc.signatureSearch, R package version 1.26.0, https://bioconductor.org/packages/signatureSearch.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, GO, GeneExpression, NetworkEnrichment, Sequencing, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), 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, readr, rhdf5, GSEABase, DelayedArray, GO.db, BiocGenerics, tibble, DOSE, AnnotationHub, stringr |
| System Requirements | C++20 |
| 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 | |
| Suggests Me | DFD |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | signatureSearch_1.26.0.tar.gz |
| Windows Binary (x86_64) | signatureSearch_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | signatureSearch_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | signatureSearch_1.26.0.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 |