cytofQC

Labels normalized cells for CyTOF data and assigns probabilities for each label

Bioconductor version: Release (3.17)

cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

Author: Jill Lundell [aut, cre] , Kelly Street [aut]

Maintainer: Jill Lundell <jflundell at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cytofQC")

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("cytofQC")

Workflow	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Annotation, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends
Imports	CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods
Linking To
Suggests	gridExtra, knitr, RColorBrewer, testthat, uwot
System Requirements
Enhances
URL	https://github.com/jillbo1000/cytofQC
Bug Reports	https://github.com/jillbo1000/cytofQC/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cytofQC_1.0.0.tar.gz
Windows Binary	cytofQC_1.0.0.zip
macOS Binary (x86_64)	cytofQC_1.0.0.tgz
macOS Binary (arm64)	cytofQC_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cytofQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cytofQC
Bioc Package Browser	https://code.bioconductor.org/browse/cytofQC/
Package Short Url	https://bioconductor.org/packages/cytofQC/
Package Downloads Report	Download Stats