Package: spillR 1.1.1

Marco Guazzini

spillR: Spillover Compensation in Mass Cytometry Data

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Authors:Marco Guazzini [aut, cre], Alexander G. Reisach [aut], Sebastian Weichwald [aut], Christof Seiler [aut]

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NEWS

# Install 'spillR' in R:

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

On BioConductor:spillR-1.1.0(bioc 3.20)spillR-1.0.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

4 exports 1.58 score 171 dependencies

Last updated 15 days agofrom:febec27581

Exports:compCytof generate_bead generate_real plotDiagnostics

Dependencies:abind ALL askpass backports beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular boot broom Cairo car carData CATALYST circlize cli clue cluster codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon curl cytolib data.table DelayedArray DelayedMatrixStats deldir digest doParallel dplyr dqrng drc fansi farver flowCore FlowSOM FNN foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggbeeswarm ggforce ggnewscale ggplot2 ggpubr ggrastr ggrepel ggridges ggsci ggsignif GlobalOptions glue gridExtra gtable gtools httr igraph IRanges irlba isoband iterators jsonlite labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mime minqa multcomp munsell mvtnorm nlme nloptr nnet nnls numDeriv openssl pbkrtest pheatmap pillar pkgconfig plotrix plyr png polyclip polynom purrr quantreg R6 ragg RColorBrewer Rcpp RcppAnnoy RcppEigen RcppHNSW RcppML RcppProgress reshape2 Rhdf5lib rjson rlang RProtoBufLib RSpectra rstatix rsvd Rtsne S4Arrays S4Vectors sandwich ScaledMatrix scales scater scuttle shape SingleCellExperiment sitmo snow SparseArray SparseM sparseMatrixStats spatstat.data spatstat.geom spatstat.utils stringi stringr SummarizedExperiment survival sys systemfonts textshaping TH.data tibble tidyr tidyselect tweenr UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr XML XVector zlibbioc zoo

spillR Vignette

Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald, Christof Seiler

Rendered fromspillR-vignette.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2024-03-18
Started: 2023-06-15

Help page	Topics
Compute spillover probability and correct for spillover	compCytof
Compute spillover probability and correct for spillover	compensate
Compute spillover probability and correct for spillover from beads only	compensate_naive
Generate dataset for vignettes and simulation studies	generate_bead
Generate dataset for vignettes and simulation studies	generate_real
Compute spillover probability and correct for spillover	plotDiagnostics
Variance stabilizing transform of counts	tfm

Package: spillR 1.1.1

spillR: Spillover Compensation in Mass Cytometry Data

spillR Vignette

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