Package: cytofQC 2.1.0

Jill Lundell

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

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.

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

cytofQC_2.1.0.tar.gz
cytofQC_2.1.0.zip(r-4.7)cytofQC_2.1.0.zip(r-4.6)cytofQC_2.1.0.zip(r-4.5)
cytofQC_2.1.0.tgz(r-4.6-any)cytofQC_2.1.0.tgz(r-4.5-any)
cytofQC_2.1.0.tar.gz(r-4.7-any)cytofQC_2.1.0.tar.gz(r-4.6-any)
cytofQC_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cytofQC/json (API)

# Install 'cytofQC' in R:

install.packages('cytofQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jillbo1000/cytofqc/issues

On BioConductor:cytofQC-2.1.0(bioc 3.24)cytofQC-2.0.0(bioc 3.23)

software singlecell annotation

4.60 score 2 stars 4 scripts 20 exports 222 dependencies

Last updated from:4b960d52e5. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	240
linux-devel-x86_64	NOTE	518
source / vignettes	OK	353
linux-release-x86_64	NOTE	502
macos-release-arm64	NOTE	225
macos-oldrel-arm64	NOTE	259
windows-devel	NOTE	351
windows-release	NOTE	380
windows-oldrel	NOTE	365
wasm-release	OK	229

Exports:cytofHist cytofQCreport gbmLabel initial initialBead initialDead initialDebris initialDoublet initialGuess label labelQC modelData plotInitialGuess probs readCytof rfLabel s3vmLabel scores svmLabel tech

Dependencies:abind ada ALL askpass assorthead backports base64enc beachmat beeswarm BH Biobase BiocGenerics biocmake BiocManager BiocNeighbors BiocParallel BiocSingular BiocStyle bitops bookdown boot broom bslib cachem car carData CATALYST caTools circlize class cli clue cluster codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon crosstalk curl cytolib data.table DelayedArray Deriv digest dir.expiry doBy doParallel dplyr dqrng drc e1071 evaluate EZtune farver fastmap filelock flowCore FlowSOM FNN fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options GA gbm generics GenomicRanges GetoptLong ggbeeswarm ggforce ggnewscale ggplot2 ggpubr ggrepel ggridges ggsci ggsignif glmnet GlobalOptions glue gplots gridExtra gtable gtools highr htmltools htmlwidgets httr igraph IRanges irlba isoband iterators jquerylib jsonlite kernlab KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa mixtools modelr multcomp mvtnorm nlme nloptr nnet nnls numDeriv openssl optimx otel pbkrtest pheatmap pillar pkgconfig plotly plotrix plyr png polyclip polynom pracma promises proxy purrr quantreg R6 randomForest rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress Rdpack reformulas reshape2 Rhdf5lib rjson rlang rmarkdown ROCR rpart RProtoBufLib RSpectra rstatix rsvd Rtsne S4Arrays S4Vectors S7 sandwich sass ScaledMatrix scales scater scuttle segmented Seqinfo shape SingleCellExperiment sitmo snow SparseArray SparseM ssc stringi stringr SummarizedExperiment survival sys systemfonts TH.data tibble tidyr tidyselect timeDate tinytex tweenr urca utf8 uwot vctrs vipor viridis viridisLite withr xfun XML XVector yaml zoo

Complete Guide to cytofQC

Rendered fromcytofQC.Rmdusingknitr::rmarkdown

Last update: 2026-01-11
Started: 2022-10-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cytofQC: Event labeling for quality control of CyTOF data	cytofQC-package cytofQC
Returns histogram for grouped data	cytofHist
Generate a cytofQC report	cytofQCreport
Returns the final label assignments for a parameter using a gradient boosting machine	gbmLabel
Preliminary bead classification	initialBead
Preliminary viability classification	initialDead
Preliminary debris classification	initialDebris
Preliminary doublet classification	initialDoublet
General preliminary classification.	initialGuess
Returns the final label assignments the specified parameters	labelQC
Returns indices for data to be used to create the final classification model	modelData
Plot preliminary classification from initialGuess	plotInitialGuess
Read in a dataset and prepare it for analysis	readCytof
Returns the final label assignments for a parameter using a random forest	rfLabel
Returns the final label assignments for a parameter using a semi-supervised support vector machine	s3vmLabel
Returns a specified object from the cytofQC SingleCellExperiment	initial label probs scores tech
Returns the final label assignments for a parameter using a support vector machine	svmLabel