recipe bioconductor-tofsims

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/tofsims.html

License

GPL-3

Recipe

/bioconductor-tofsims/meta.yaml

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.

package bioconductor-tofsims

Versions

1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.1-0, 1.10.0-0

Depends

• bioconductor-protgenerics >=1.20.0,<1.21.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-als

• r-base >=4.0,<4.1.0a0

• r-chemometricswithr

• r-kernsmooth

• r-rcpp >=0.11.2

• r-rcpparmadillo

• r-signal

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-tofsims

and update with:

conda update bioconductor-tofsims

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tofsims:<tag>

(see bioconductor-tofsims/tags for valid values for <tag>)

Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tofsims/README.html)