tofsims

DOI: 10.18129/B9.bioc.tofsims    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Workflow with the `tofsims` package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 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
Links To Me
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
Package Short Url	https://bioconductor.org/packages/tofsims/
Package Downloads Report	Download Stats