spillR

This is the development version of spillR; for the stable release version, see spillR.

Spillover Compensation in Mass Cytometry Data

Bioconductor version: Development (3.21)

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] (ORCID: ), Alexander G. Reisach [aut] (ORCID: ), Sebastian Weichwald [aut] (ORCID: ), Christof Seiler [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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
NEWS	Text

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Details

biocViews	FlowCytometry, ImmunoOncology, MassSpectrometry, Preprocessing, Regression, SingleCell, Software, StatisticalMethod, Visualization
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	LGPL-3
Depends	R (>= 4.3.0), SummarizedExperiment, CATALYST
Imports	dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel
System Requirements
URL

Suggests	knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin
Linking To
Enhances
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	spillR_1.3.0.tar.gz
Windows Binary (x86_64)	spillR_1.3.0.zip
macOS Binary (x86_64)	spillR_1.3.0.tgz
macOS Binary (arm64)	spillR_1.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spillR
Source Repository (Developer Access)	git clone [email protected]:packages/spillR
Bioc Package Browser	https://code.bioconductor.org/browse/spillR/
Package Short Url	https://bioconductor.org/packages/spillR/
Package Downloads Report	Download Stats