tofsims

DOI: 10.18129/B9.bioc.tofsims    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 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: 3.15

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>

Installation

To install this package, start R (version "4.2") 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

PDF		Reference Manual

Details

biocViews	DataImport, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 years)
License	GPL-3
Depends	R (>= 3.3.0), methods, utils, ProtGenerics
Imports	Rcpp (>= 0.11.2), ALS, alsace, 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/tofsims
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tofsims
Package Short Url	https://bioconductor.org/packages/tofsims/
Package Downloads Report	Download Stats