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SPUTNIK  

Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit
View on CRAN: Click here


Download and install SPUTNIK package within the R console
Install from CRAN:
install.packages("SPUTNIK")

Install from Github:
library("remotes")
install_github("cran/SPUTNIK")

Install by package version:
library("remotes")
install_version("SPUTNIK", "1.4.2")



Attach the package and use:
library("SPUTNIK")
Maintained by
Paolo Inglese
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-02-19
Latest Update: 2023-11-07
Description:
Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) <doi:10.1093/bioinformatics/bty622>.
How to cite:
Paolo Inglese (2018). SPUTNIK: Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit. R package version 1.4.2, https://cran.r-project.org/web/packages/SPUTNIK. Accessed 04 Jan. 2025.
Previous versions and publish date:
1.0.0 (2018-02-19 10:17), 1.0.1 (2018-02-23 10:14), 1.0.2 (2018-03-30 14:16), 1.0.3.1 (2018-07-20 12:50), 1.0.3.2 (2018-08-15 23:40), 1.0.3.3 (2018-08-22 14:40), 1.0.3.4 (2018-09-18 15:50), 1.0.3 (2018-07-20 12:40), 1.0.4.1 (2018-10-08 15:50), 1.1.1 (2018-10-25 23:50), 1.1.2 (2019-04-16 22:32), 1.1 (2018-10-23 13:50), 1.3.1 (2021-02-01 11:00), 1.3.2 (2021-03-23 01:50), 1.3.3 (2021-05-18 01:10), 1.3 (2020-03-23 15:20), 1.4.1 (2022-11-24 11:00), 1.4 (2021-10-19 00:30)
Other packages that cited SPUTNIK R package
View SPUTNIK citation profile
Other R packages that SPUTNIK depends, imports, suggests or enhances
Complete documentation for SPUTNIK
Functions, R codes and Examples using the SPUTNIK R package
Some associated functions: CSRPeaksFilter . NMI . PCAImage-msi.dataset-method . SSIM . applyPeaksFilter-msi.dataset-method . binKmeans-msi.dataset-method . binKmeans2-msi.dataset-method . binOtsu-ms.image-method . binSupervised-msi.dataset-method . bladderMALDIRompp2010 . closeImage-ms.image-method . countPixelsFilter . createPeaksFilter . getIntensityMat-msi.dataset-method . getMZ-msi.dataset-method . getShapeMSI-msi.dataset-method . gini.index . globalPeaksFilter . invertImage-ms.image-method . ms.image-class . msImage . msi.dataset-class . msiDataset . normIntensity-msi.dataset-method . numDetectedMSI-msi.dataset-method . ovarianDESIDoria2016 . plot . refImageBinaryKmeans . refImageBinaryKmeansMulti . refImageBinaryOtsu . refImageBinarySVM . refImageContinuous . removeSmallObjects-ms.image-method . scatter.ratio . smoothImage-ms.image-method . spatial.chaos . splitPeaksFilter . totalIonCountMSI-msi.dataset-method . varTransform-msi.dataset-method . 
Some associated R codes: add_rem_border.R . binary_refimg.R . construct_funcs.R . continuous_refimg.R . data_funcs.R . filter_count.R . filter_csr.R . filter_global.R . filter_split.R . generic_funcs.R . graph_funcs.R . is_funcs.R . ms.image_class.R . ms.image_methods.R . msi.dataset_class.R . msi.dataset_funcs.R . msi.dataset_methods.R . mz_funcs.R . sparseness_funcs.R .  Full SPUTNIK package functions and examples
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