Introduction | Setting up the data | Mocking up a data set | Pre-processing of intensities | Pooling cells together | Estimating transformation parameters | Gating out uninteresting cells | Applying functions to the original data | Normalizing intensities across batches | Counting cells into hyperspheres | Testing for significant differences in abundance | Controlling the spatial FDR | Visualizing and interpreting the results | With static plots | Using a Shiny app | Additional notes | Session information
Package: cydar 1.37.0
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:
cydar_1.37.0.tar.gz
cydar_1.37.0.zip(r-4.7)cydar_1.37.0.zip(r-4.6)cydar_1.37.0.zip(r-4.5)
cydar_1.37.0.tgz(r-4.6-x86_64)cydar_1.37.0.tgz(r-4.6-arm64)cydar_1.37.0.tgz(r-4.5-x86_64)cydar_1.37.0.tgz(r-4.5-arm64)
cydar_1.37.0.tar.gz(r-4.7-arm64)cydar_1.37.0.tar.gz(r-4.7-x86_64)cydar_1.37.0.tar.gz(r-4.6-arm64)cydar_1.37.0.tar.gz(r-4.6-x86_64)
cydar_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cydar/json (API)
| # Install 'cydar' in R: |
| install.packages('cydar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:cydar-1.37.0(bioc 3.24)cydar-1.36.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyflowcytometrymultiplecomparisonproteomicssinglecellcpp
Last updated from:363374650d. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 222 | ||
| linux-devel-arm64 | NOTE | 362 | ||
| linux-devel-x86_64 | NOTE | 380 | ||
| source / vignettes | OK | 381 | ||
| linux-release-arm64 | NOTE | 341 | ||
| linux-release-x86_64 | NOTE | 376 | ||
| macos-release-arm64 | NOTE | 209 | ||
| macos-release-x86_64 | NOTE | 382 | ||
| macos-oldrel-arm64 | NOTE | 216 | ||
| macos-oldrel-x86_64 | NOTE | 544 | ||
| windows-devel | NOTE | 325 | ||
| windows-release | NOTE | 321 | ||
| windows-oldrel | NOTE | 319 | ||
| wasm-release | OK | 212 |
Exports:cbindcellAssignmentscellInformationcellIntensitiescountCellscreateColorBardnaGateexpandRadiusfindFirstSpheregetCenterCellintensitiesintensityRangesinterpretSphereslabelSpheresmarkernamesmedIntensitiesmultiIntHistneighborDistancesnormalizeBatchoutlierGatepickBestMarkersplotSphereIntensityplotSphereLogFCpoolCellsprepareCellDatashowspatialFDR
Dependencies:abindassortheadbase64encbeachmatBHBiobaseBiocGenericsbiocmakeBiocNeighborsBiocParallelbslibcachemclicodetoolscommonmarkcpp11cytolibDelayedArraydigestdir.expiryfarverfastmapfilelockflowCorefontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehtmltoolshttpuvIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeotelpromisesR6rappdirsRColorBrewerRcppRhdf5librlangRProtoBufLibS4ArraysS4VectorsS7sassscalesSeqinfoshinySingleCellExperimentsnowsourcetoolsSparseArraySummarizedExperimentvctrsviridisviridisLitewithrxtableXVector
