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:
Maintainer: Marco Guazzini <m.guazzini at student.maastrichtuniversity.nl>
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 | ||
| NEWS | Text |
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 |
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_1.3.0.tar.gz |
| Windows Binary (x86_64) | spillR_1.3.0.zip |
| macOS Binary (x86_64) | spillR_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |