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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineOB")
In most cases, you don't need to download the package archive at all.
ChemmineOB
R interface to a subset of OpenBabel functionalities
Bioconductor version: 3.0
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: Kevin Horan <khoran at cs.ucr.edu>
Citation (from within R,
enter citation("ChemmineOB")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineOB")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChemmineOB")
| HTML | R Script | ChemmineOB |
| Reference Manual | ||
| Text | README | |
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Cheminformatics, Software |
| Version | 1.4.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | file LICENSE |
| Depends | R (>= 2.15.1), methods |
| Imports | BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) |
| LinkingTo | BH, Rcpp |
| Suggests | ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap |
| SystemRequirements | OpenBabel (>= 2.3.1) with headers. http://openbabel.org |
| Enhances | ChemmineR(>= 2.13.0) |
| URL | http://manuals.bioinformatics.ucr.edu/home/chemminer |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ChemmineR |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChemmineOB_1.4.1.tar.gz |
| Windows Binary | ChemmineOB_1.4.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ChemmineOB_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | ChemmineOB_1.4.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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