spillR
This is thereleased version of spillR; for the devel version, seespillR.
Spillover Compensation in Mass Cytometry Data
Bioconductor version: Release (3.22)
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: 0009-0007-8111-5772, Alexander G. Reisach [aut] ORCID: 0009-0003-5057-6278, Sebastian Weichwald [aut] ORCID: 0000-0003-0169-7244, Christof Seiler [aut] ORCID: 0000-0001-8802-3642
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")BiocManager::install("spillR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.6.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | spillR_1.6.0.tar.gz |
| Windows Binary (x86_64) | spillR_1.6.0.zip |
| macOS Binary (x86_64) | spillR_1.6.0.tgz |
| macOS Binary (arm64) | spillR_1.6.0.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 |