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

DOI: 10.18129/B9.bioc.tofsims    

This is the development version of tofsims; for the stable release version, see tofsims.

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Bioconductor version: Development (3.7)

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
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, ImagingMassSpectrometry, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.7.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
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 https://github.com/lorenzgerber/tofsims
BugReports https://github.com/lorenzgerber/tofsims/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tofsims_1.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) tofsims_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tofsims
Package Short Url http://bioconductor.org/packages/tofsims/
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