cytofQC
Labels normalized cells for CyTOF data and assigns probabilities for each label
Bioconductor version: Release (3.20)
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("cytofQC")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, SingleCell, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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 | |
| 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 | cytofQC_1.6.0.tar.gz |
| Windows Binary (x86_64) | cytofQC_1.6.0.zip |
| macOS Binary (x86_64) | cytofQC_1.6.0.tgz |
| macOS Binary (arm64) | cytofQC_1.5.0.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 |