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")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cytofQC")
HTML | R Script | Workflow |
Reference Manual | ||
Text | NEWS |
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 |
LinkingTo | |
Suggests | gridExtra, knitr, RColorBrewer, testthat, uwot |
SystemRequirements | |
Enhances | |
URL | https://github.com/jillbo1000/cytofQC |
BugReports | https://github.com/jillbo1000/cytofQC/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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 |
Old Source Packages for BioC 3.17 | Source Archive |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: