ChemmineOB
This is the released version of ChemmineOB; for the devel version, see ChemmineOB.
R interface to a subset of OpenBabel functionalities
Bioconductor version: Release (3.23)
ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.
Author: Kevin Horan, Thomas Girke
Maintainer: Thomas Girke <thomas.girke at ucr.edu>
citation("ChemmineOB")):
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("ChemmineOB")
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("ChemmineOB")| ChemmineOB | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization |
| Version | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.1), methods |
| Imports | BiocGenerics, Rcpp (>= 0.11.0) |
| System Requirements | OpenBabel (>= 3.0.0) with headers (http://openbabel.org). Eigen3 with headers. |
| URL | https://github.com/girke-lab/ChemmineOB |
See More
| Suggests | ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown, RUnit, codetools |
| Linking To | BH, Rcpp |
| Enhances | ChemmineR(>= 2.13.0) |
| 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 | ChemmineOB_1.50.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | ChemmineOB_1.49.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ChemmineOB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChemmineOB |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChemmineOB/ |
| Package Short Url | https://bioconductor.org/packages/ChemmineOB/ |
| Package Downloads Report | Download Stats |