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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tofsims")
In most cases, you don't need to download the package archive at all.
tofsims
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see tofsims.
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Bioconductor version: 3.4
This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing package EBImage offers image segmentation functionality.
Author: Lorenz Gerber, Viet Mai Hoang
Maintainer: Lorenz Gerber <genfys at gmail.com>
Citation (from within R,
enter citation("tofsims")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tofsims")
Documentation
| HTML | R Script | Workflow with the `tofsims` package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, ImagingMassSpectrometry, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| License | GPL-3 |
| Depends | R (>= 3.3.0), methods, utils, ProtGenerics |
| Imports | Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth, graphics, grDevices, stats |
| LinkingTo | Rcpp, RcppArmadillo |
| Suggests | EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | tofsims_1.2.0.tar.gz |
| Windows Binary | tofsims_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | tofsims_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/tofsims/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/tofsims/ |
| Package Downloads Report | Download Stats |
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