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("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 | ||
| 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 |