spillR
Spillover Compensation in Mass Cytometry Data
Bioconductor version: Release (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("spillR")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
NEWS | Text |
Details
biocViews | FlowCytometry, ImmunoOncology, MassSpectrometry, Preprocessing, Regression, SingleCell, Software, StatisticalMethod, Visualization |
Version | 1.0.1 |
In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
License | LGPL-3 |
Depends | R (>= 4.3.0), SummarizedExperiment, CATALYST |
Imports | dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel |
System Requirements | |
URL |
See More
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_1.0.1.tar.gz |
Windows Binary | spillR_1.0.1.zip |
macOS Binary (x86_64) | spillR_1.0.1.tgz |
macOS Binary (arm64) | spillR_1.0.1.tgz |
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 |
Old Source Packages for BioC 3.19 | Source Archive |