signatureSearch
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Bioconductor version: Release (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 (from within R, enter
citation("signatureSearch")):
Installation
To install this package, start R (version "4.4") 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, KEGG, NetworkEnrichment, Sequencing, Software |
| Version | 1.20.0 |
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | signatureSearch_1.20.0.zip |
| macOS Binary (x86_64) | signatureSearch_1.20.0.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 |