bioassayR
This is the released version of bioassayR; for the devel version, see bioassayR.
Cross-target analysis of small molecule bioactivity
Bioconductor version: Release (3.23)
bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
Author: Tyler Backman, Ronly Schlenk, Thomas Girke
Maintainer: Thomas Girke <tgirke at citrus.ucr.edu>
citation("bioassayR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bioassayR")
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("bioassayR")| bioassayR Introduction and Examples | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bioinformatics, CellBasedAssays, DataImport, ImmunoOncology, Infrastructure, Metabolomics, MicrotitrePlateAssay, Proteomics, Software, Visualization |
| Version | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics(>= 0.13.8) |
| Imports | XML, ChemmineR |
| System Requirements | |
| URL | https://github.com/girke-lab/bioassayR |
| Bug Reports | https://github.com/girke-lab/bioassayR/issues |
See More
| Suggests | BiocStyle, RCurl, biomaRt, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | bioassayR_1.50.0.tar.gz |
| Windows Binary (x86_64) | bioassayR_1.50.0.zip |
| macOS Binary (big-sur-x86_64) | bioassayR_1.50.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/bioassayR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bioassayR |
| Bioc Package Browser | https://code.bioconductor.org/browse/bioassayR/ |
| Package Short Url | https://bioconductor.org/packages/bioassayR/ |
| Package Downloads Report | Download Stats |