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cytofQC

This is the development version of cytofQC; for the stable release version, see cytofQC.

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
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
See More
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_1.1.0.tar.gz
Windows Binary cytofQC_1.1.0.zip
macOS Binary (x86_64) cytofQC_1.1.0.tgz
macOS Binary (arm64) cytofQC_1.1.0.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