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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineR")
In most cases, you don't need to download the package archive at all.
ChemmineR
Cheminformatics Toolkit for R
Bioconductor version: 3.0
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Maintainer: ChemmineR Team <khoran at cs.ucr.edu>
Citation (from within R,
enter citation("ChemmineR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChemmineR")
| HTML | R Script | ChemmineR |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | CellBasedAssays, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Proteomics, Software, Visualization |
| Version | 2.18.1 |
| In Bioconductor since | BioC 2.3 (R-2.8) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods |
| Imports | rjson, graphics, methods, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0) |
| LinkingTo | Rcpp |
| Suggests | RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB(>= 1.3.8), ChemmineDrugs |
| SystemRequirements | |
| Enhances | ChemmineOB, ChemmineDrugs |
| URL | http://manuals.bioinformatics.ucr.edu/home/chemminer |
| Depends On Me | ChemmineDrugs, eiR, fmcsR |
| Imports Me | eiR, fmcsR, Rchemcpp, Rcpi |
| Suggests Me | bioassayR, ChemmineOB |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChemmineR_2.18.1.tar.gz |
| Windows Binary | ChemmineR_2.18.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ChemmineR_2.18.1.tgz |
| Mac OS X 10.9 (Mavericks) | ChemmineR_2.18.1.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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