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 (3.15)

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>

Citation (from within R, enter citation("tofsims")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.23.0
In Bioconductor since BioC 3.3 (R-3.3) (5.5 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
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
Windows Binary
macOS 10.13 (High Sierra)
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/
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