Package: spillR 1.8.0

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]

spillR_1.8.0.tar.gz
spillR_1.8.0.zip(r-4.7)spillR_1.8.0.zip(r-4.6)spillR_1.8.0.zip(r-4.5)
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spillR_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spillR/json (API)

# Install 'spillR' in R:

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

On BioConductor:spillR-1.9.0(bioc 3.24)spillR-1.8.0(bioc 3.23)

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

flowcytometry immunooncology massspectrometry preprocessing singlecell software statisticalmethod visualization regression

4.00 score 3 scripts 245 downloads 4 exports 169 dependencies

Last updated from:334288ff24 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	225
linux-devel-x86_64	OK	487
source / vignettes	OK	403
linux-release-x86_64	OK	483
macos-release-arm64	OK	428
macos-oldrel-arm64	OK	219
windows-devel	OK	411
windows-release	OK	436
windows-oldrel	OK	450
wasm-release	OK	191

Exports:compCytof generate_bead generate_real plotDiagnostics

Dependencies:abind ALL assorthead backports base64enc beachmat beeswarm BH Biobase BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular boot broom car carData CATALYST circlize cli clue cluster codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon cytolib DelayedArray Deriv digest dir.expiry doBy doParallel dplyr dqrng drc farver filelock flowCore FlowSOM FNN foreach forecast formatR Formula fracdiff futile.logger futile.options generics GenomicRanges GetoptLong ggbeeswarm ggforce ggnewscale ggplot2 ggpubr ggrepel ggridges ggsci ggsignif GlobalOptions glue gridExtra gtable gtools igraph IRanges irlba isoband iterators jsonlite labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv minqa modelr multcomp mvtnorm nlme nloptr nnet nnls numDeriv pbkrtest pheatmap pillar pkgconfig plotrix plyr png polyclip polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress Rdpack reformulas reshape2 Rhdf5lib rjson rlang RProtoBufLib RSpectra rstatix rsvd Rtsne S4Arrays S4Vectors S7 sandwich ScaledMatrix scales scater scuttle Seqinfo shape SingleCellExperiment sitmo snow SparseArray SparseM spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival systemfonts TH.data tibble tidyr tidyselect timeDate tweenr urca utf8 uwot vctrs vipor viridis viridisLite withr XML XVector zoo

spillR Vignette

Rendered fromspillR-vignette.Rmdusingknitr::rmarkdown

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 1.8.0

spillR: Spillover Compensation in Mass Cytometry Data

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