Package: cydar 1.31.0

Aaron Lun

cydar: Using Mass Cytometry for Differential Abundance Analyses

Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

Authors:Aaron Lun [aut, cre]

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NEWS

# Install 'cydar' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:cydar-1.31.0(bioc 3.21)cydar-1.30.0(bioc 3.20)

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

immunooncology flowcytometry multiplecomparison proteomics singlecell cpp

5.64 score 48 scripts 258 downloads 6 mentions 27 exports 91 dependencies

Last updated 4 months agofrom:8dc413ed52. Checks:1 OK, 8 NOTE, 2 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 08 2025
R-4.5-win-x86_64	NOTE	Feb 08 2025
R-4.5-mac-x86_64	WARNING	Feb 08 2025
R-4.5-mac-aarch64	WARNING	Feb 08 2025
R-4.5-linux-x86_64	NOTE	Feb 08 2025
R-4.4-win-x86_64	NOTE	Feb 08 2025
R-4.4-mac-x86_64	NOTE	Feb 08 2025
R-4.4-mac-aarch64	NOTE	Feb 08 2025
R-4.3-win-x86_64	NOTE	Feb 08 2025
R-4.3-mac-x86_64	NOTE	Feb 08 2025
R-4.3-mac-aarch64	NOTE	Dec 10 2024

Exports:cbind cellAssignments cellInformation cellIntensities countCells createColorBar dnaGate expandRadius findFirstSphere getCenterCell intensities intensityRanges interpretSpheres labelSpheres markernames medIntensities multiIntHist neighborDistances normalizeBatch outlierGate pickBestMarkers plotSphereIntensity plotSphereLogFC poolCells prepareCellData show spatialFDR

Dependencies:abind askpass assorthead base64enc BH Biobase BiocGenerics BiocNeighbors BiocParallel bslib cachem cli codetools colorspace commonmark cpp11 crayon curl cytolib DelayedArray digest fansi farver fastmap flowCore fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable htmltools httpuv httr IRanges isoband jquerylib jsonlite labeling lambda.r later lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig promises R6 rappdirs RColorBrewer Rcpp Rhdf5lib rlang RProtoBufLib S4Arrays S4Vectors sass scales shiny SingleCellExperiment snow sourcetools SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridis viridisLite withr xtable XVector

Detecting differentially abundant subpopulations in mass cytometry data

Aaron Lun

Rendered fromcydar.Rmdusingknitr::rmarkdownon Feb 08 2025.

Last update: 2024-09-06
Started: 2017-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Count cells in high-dimensional space	countCells
Create a color bar	createColorBar
CyData class and methods	cbind,CyData-method cellAssignments cellInformation cellIntensities CyData CyData-class getCenterCell intensities markernames markernames,CyData-method show,CyData-method [,CyData,ANY,ANY,ANY-method [<-,CyData,ANY,ANY,CyData-method
Gate events based on DNA channels	dnaGate
Expand the hypersphere radius	expandRadius
Identifies the first non-redundant hyperspheres	findFirstSphere
Define intensity ranges	intensityRanges
Interactive interpretation of hyperspheres	interpretSpheres
Label unannotated hyperspheres	labelSpheres
Compute median marker intensities	medIntensities
multiIntHist	multiIntHist
Compute distances to neighbors	neighborDistances
Normalize intensities across batches	normalizeBatch
Create an outlier gate	outlierGate
Pick best markers	pickBestMarkers
Plot cell or hypersphere data	plotSphereIntensity
Plot changes in hypersphere abundance	plotSphereLogFC
Pool cells for pre-processing	poolCells
Prepare mass cytometry data	prepareCellData
Compute the spatial FDR	spatialFDR