tofsims

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tofsims")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tofsims")
Workflow with the `tofsims` package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.12.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 3.3.0), methods, utils, ProtGenerics
Imports Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth, graphics, grDevices, stats
System Requirements
URL https://github.com/lorenzgerber/tofsims
Bug Reports https://github.com/lorenzgerber/tofsims/issues
See More
Suggests EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer
Linking To Rcpp, RcppArmadillo
Enhances parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package tofsims_1.12.0.tar.gz
Windows Binary tofsims_1.12.0.zip
Mac OS X 10.11 (El Capitan) tofsims_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tofsims
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tofsims
Bioc Package Browser https://code.bioconductor.org/browse/tofsims/
Package Short Url https://bioconductor.org/packages/tofsims/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive