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spillR

This is the development version of spillR; to use it, please install the devel version of Bioconductor.

Spillover Compensation in Mass Cytometry Data


Bioconductor version: Development (3.19)

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Author: Marco Guazzini [aut, cre] , Alexander G. Reisach [aut], Sebastian Weichwald [aut] , Christof Seiler [aut]

Maintainer: Marco Guazzini <m.guazzini at student.maastrichtuniversity.nl>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("spillR")

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("spillR")
spillR Vignette HTML R Script
Reference Manual PDF

Details

biocViews FlowCytometry, ImmunoOncology, MassSpectrometry, Preprocessing, Regression, SingleCell, Software, StatisticalMethod, Visualization
Version 0.99.10
In Bioconductor since BioC 3.19 (R-4.4)
License LGPL-3
Depends R (>= 4.3.0), SummarizedExperiment, CATALYST
Imports dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.geom, S4Vectors, parallel
System Requirements
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Suggests knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spillR_0.99.10.tar.gz
Windows Binary spillR_0.99.10.zip
macOS Binary (x86_64) spillR_0.99.10.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/spillR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spillR
Bioc Package Browser https://code.bioconductor.org/browse/spillR/
Package Short Url https://bioconductor.org/packages/spillR/
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