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

Need some help? Ask on the Bioconductor Support site!

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)
macOS Binary (x86_64)
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/
Package Downloads Report	Download Stats