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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RMassBank")
In most cases, you don't need to download the package archive at all.
RMassBank
Workflow to process tandem MS files and build MassBank records
Bioconductor version: 3.0
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Author: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze
Maintainer: RMassBank at Eawag <massbank at eawag.ch>
Citation (from within R,
enter citation("RMassBank")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RMassBank")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RMassBank")
| R Script | RMassBank non-standard usage | |
| R Script | RMassBank using XCMS walkthrough | |
| R Script | RMassBank walkthrough | |
| Reference Manual |
Details
| biocViews | Bioinformatics, MassSpectrometry, Metabolomics, Software |
| Version | 1.8.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | Rcpp |
| Imports | XML, RCurl, rjson, rcdk, yaml, mzR, methods |
| LinkingTo | |
| Suggests | gplots, RMassBankData, xcms(>= 1.37.1), CAMERA, ontoCAT, RUnit |
| SystemRequirements | OpenBabel |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RMassBankData |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RMassBank_1.8.1.tar.gz |
| Windows Binary | RMassBank_1.8.1.zip |
| Mac OS X 10.6 (Snow Leopard) | RMassBank_1.8.1.tgz |
| Mac OS X 10.9 (Mavericks) | RMassBank_1.8.1.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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