ChemmineR
This is the released version of ChemmineR; for the devel version, see ChemmineR.
Cheminformatics Toolkit for R
Bioconductor version: Release (3.23)
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: Thomas Girke <thomas.girke at ucr.edu>
citation("ChemmineR")):
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("ChemmineR")
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("ChemmineR")| ChemmineR | HTML | R Script |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization |
| Version | 3.64.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (18 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods |
| Imports | rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2, grid, gridExtra, png, base64enc, DT, rsvg, jsonlite, stringi |
| System Requirements | GNU make |
| URL | https://github.com/girke-lab/ChemmineR |
See More
| Suggests | RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png, rmarkdown, BiocManager, bibtex, codetools |
| Linking To | Rcpp, BH |
| Enhances | ChemmineOB |
| Depends On Me | eiR, fmcsR, ChemmineDrugs |
| Imports Me | bioassayR, CompoundDb, customCMPdb, eiR, fmcsR, MetID, RMassBank, chemodiv |
| Suggests Me | ChemmineOB, xnet |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChemmineR_3.64.0.tar.gz |
| Windows Binary (x86_64) | ChemmineR_3.64.0.zip |
| macOS Binary (big-sur-x86_64) | ChemmineR_3.64.0.tgz |
| macOS Binary (sonoma-arm64) | ChemmineR_3.64.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChemmineR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChemmineR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChemmineR/ |
| Package Short Url | https://bioconductor.org/packages/ChemmineR/ |
| Package Downloads Report | Download Stats |