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 (3.20)
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")
):
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 | ||
NEWS | Text |
Details
biocViews | Coverage, DifferentialExpression, GO, GeneExpression, KEGG, NetworkEnrichment, Sequencing, Software |
Version | 1.19.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (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_1.19.0.tar.gz |
Windows Binary | signatureSearch_1.19.0.zip |
macOS Binary (x86_64) | signatureSearch_1.19.0.tgz |
macOS Binary (arm64) | signatureSearch_1.19.0.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 |