Package: cytofQC 1.5.0

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_1.5.0.tar.gz
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cytofQC_1.5.0.tgz(r-4.4-any)cytofQC_1.5.0.tgz(r-4.3-any)
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cytofQC.pdf |cytofQC.html✨
cytofQC/json (API)
NEWS

# 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-1.5.0(bioc 3.20)cytofQC-1.4.0(bioc 3.19)

bioconductor-package

20 exports 0.49 score 231 dependencies

Last updated 2 months agofrom:dd1933b8a9

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 backports base64enc beachmat beeswarm BH Biobase BiocGenerics BiocManager BiocNeighbors BiocParallel BiocSingular BiocStyle bitops bookdown boot broom bslib cachem Cairo car carData CATALYST caTools circlize class cli clue cluster codetools colorRamps colorspace commonmark ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon crul curl cytolib data.table DelayedArray DelayedMatrixStats Deriv digest doBy doParallel dplyr dqrng drc e1071 evaluate extrafont extrafontdb EZtune fansi farver fastmap flowCore FlowSOM FNN fontawesome fontBitstreamVera fontLiberation fontquiver foreach formatR fs futile.logger futile.options GA gbm gdtools generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong gfonts ggbeeswarm ggforce ggnewscale ggplot2 ggpubr ggrastr ggrepel ggridges ggsci ggsignif glmnet GlobalOptions glue gplots gridExtra gtable gtools highr hrbrthemes htmltools httpcode httpuv httr igraph IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcomp munsell mvtnorm nlme nloptr nnet nnls numDeriv openssl optimx pbkrtest pheatmap pillar pkgconfig plotrix plyr png polyclip polynom pracma promises proxy purrr quantreg R6 ragg randomForest rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress reshape2 Rhdf5lib rjson rlang rmarkdown ROCR rpart RProtoBufLib RSpectra rstatix rsvd Rtsne Rttf2pt1 S4Arrays S4Vectors sandwich sass ScaledMatrix scales scater scuttle shape shiny SingleCellExperiment sitmo snow sourcetools SparseArray SparseM sparseMatrixStats ssc stringi stringr SummarizedExperiment survival sys systemfonts textshaping TH.data tibble tidyr tidyselect tinytex triebeard tweenr UCSC.utils urltools utf8 uwot vctrs vipor viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc zoo

Complete Guide to cytofQC

Rendered fromcytofQC.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-03-15
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