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cytofQC

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


Bioconductor version: Release (3.18)

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 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends
Imports CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods
System Requirements
URL https://github.com/jillbo1000/cytofQC
Bug Reports https://github.com/jillbo1000/cytofQC/issues
See More
Suggests gridExtra, knitr, RColorBrewer, testthat, uwot
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package cytofQC_1.2.0.tar.gz
Windows Binary cytofQC_1.2.0.zip
macOS Binary (x86_64) cytofQC_1.2.0.tgz
macOS Binary (arm64) cytofQC_1.2.0.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