To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("fmcsR")
In most cases, you don't need to download the package archive at all.
fmcsR
Mismatch Tolerant Maximum Common Substructure Searching
Bioconductor version: 3.0
The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.
Author: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke
Maintainer: ChemmineR Team <see at url>
Citation (from within R,
enter citation("fmcsR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("fmcsR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("fmcsR")
| HTML | R Script | fmcsR |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | CellBasedAssays, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Proteomics, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), ChemmineR, methods |
| Imports | RUnit, methods, ChemmineR, BiocGenerics, parallel |
| LinkingTo | |
| Suggests | BiocStyle, knitr, knitcitations, knitrBootstrap |
| SystemRequirements | |
| Enhances | |
| URL | http://manuals.bioinformatics.ucr.edu/home/chemminer |
| Depends On Me | |
| Imports Me | Rcpi |
| Suggests Me | ChemmineR |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | fmcsR_1.8.0.tar.gz |
| Windows Binary | fmcsR_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | fmcsR_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | fmcsR_1.8.0.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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