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

   

This package is for version 3.3 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: 3.3

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 1.0.2
In Bioconductor since BioC 3.3 (R-3.3) (< 6 months)
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_1.0.2.tar.gz
Windows Binary tofsims_1.0.2.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) tofsims_1.0.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/tofsims/tree/release-3.3
Package Short Url http://bioconductor.org/packages/tofsims/
Package Downloads Report Download Stats

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