bioassayR

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see bioassayR.

Cross-target analysis of small molecule bioactivity

Bioconductor version: 3.10

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: Tyler Backman <tbackman at lbl.gov>

Citation (from within R, enter citation("bioassayR")):

Installation

To install this package, start R (version "3.6") 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")

Introduction and Examples HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bioinformatics, CellBasedAssays, DataImport, ImmunoOncology, Infrastructure, Metabolomics, MicrotitrePlateAssay, Proteomics, Software, Visualization

Version 1.24.0

In Bioconductor since BioC 2.13 (R-3.0) (10.5 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/TylerBackman/bioassayR

Bug Reports https://github.com/TylerBackman/bioassayR/issues

Suggests BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package bioassayR_1.24.0.tar.gz

Windows Binary bioassayR_1.24.0.zip

Mac OS X 10.11 (El Capitan) bioassayR_1.24.0.tgz

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

Old Source Packages for BioC 3.10 Source Archive