Package: COMPASS 1.43.0

Greg Finak

COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

Authors:Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde

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COMPASS.pdf |COMPASS.html✨
COMPASS/json (API)
NEWS

# Install 'COMPASS' in R:
install.packages('COMPASS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rglab/compass/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • CC - Simulated COMPASSContainer
  • CR - Simulated COMPASS fit

On BioConductor:COMPASS-1.43.0(bioc 3.20)COMPASS-1.42.0(bioc 3.19)

bioconductor-package

35 exports 6.23 score 65 dependencies 614 mentions

Last updated 2 months agofrom:a127bb6b3a

Exports:categoriesCellCountsCombinationsCOMPASSCOMPASSContainerCOMPASSContainerFromGatingSetCOMPASSDescriptionCOMPASSDescription<-COMPASSfitToCountsTableCOMPASSMCMCDiagnosisFunctionalityScoregetCountsGetThresholdedIntensitiesmarkersmetadatametadata<-pheatmapplot2plotCOMPASSResultStackPolyfunctionalityScorePosteriorPosteriorDiffPosteriorLogDiffPosteriorPsPosteriorPuResponsescoresselect_compass_popsshinyCOMPASSshinyCOMPASSDepsSimpleCOMPASSTotalCellCountstranslate_marker_namestranspose_listUniqueCombinations

Dependencies:abindbase64encBiocManagerBiocStylebookdownbslibcachemcliclueclustercodacodetoolscolorspacecpp11data.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsgluehighrhtmltoolsiteratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrmemoisemimemunsellpdistpillarpkgconfigplyrpurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalesstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells)COMPASS-package
Categoriescategories
Compute Number of Cells Positive for Certain Cytokine CombinationsCellCounts
Generate CombinationsCombinations
Fit the COMPASS ModelCOMPASS
Generate the Data Object used by COMPASSCOMPASSContainer
Simulated COMPASSContainerCC COMPASSContainer-data
Create a COMPASS Container from a GatingSetCOMPASSContainerFromGatingSet
Get and Set the Description for the Shiny ApplicationCOMPASSDescription COMPASSDescription<-
Extract a table of counts from a COMPASSResult objectCOMPASSfitToCountsTable
Diagnostic of a set of COMPASS Models.COMPASSMCMCDiagnosis
COMPASSResult AccessorsCOMPASSResult-accessors Gamma MeanGamma
Simulated COMPASS fitCOMPASSResult-data CR
Compute the Functionality Score for each subject fit in a COMPASS modelFunctionalityScore FunctionalityScore.COMPASSResult FunctionalityScore.default
Get a data.table of counts of polyfunctional subsetsgetCounts
Extract Thresholded Intensities from a GatingSetGetThresholdedIntensities
Markersmarkers
Make a 'Wide' data set 'Long'melt_ melt_.data.frame melt_.matrix
Merge Two COMPASSContainersmerge.COMPASSContainer
Metadatametadata metadata.COMPASSContainer metadata.COMPASSResult metadata<- metadata<-.COMPASSContainer
A function to draw clustered heatmaps.pheatmap
Plot a COMPASSResultplot plot.COMPASSResult
Plot a pair of COMPASSResultsplot2
Plot multiple COMPASSResultsplotCOMPASSResultStack
Compute the Polyfunctionality Score for each subject fit in a COMPASS modelPolyfunctionalityScore PolyfunctionalityScore.COMPASSResult PolyfunctionalityScore.default
Retrieve Posterior Measures from a COMPASS fitPosterior PosteriorDiff PosteriorLogDiff PosteriorPs PosteriorPu
Print a COMPASSContainer Objectprint.COMPASSContainer
Print a COMPASSResult Objectprint.COMPASSResult
Compute a response probability from COMPASS mcmc samples.Response Response.COMPASSResult
Fetch the table of scores and metadata from a COMPASSResult Objectscores
Flag COMPASS boolean populationsselect_compass_pops
Start a Shiny Application for Visualizing COMPASS ResultsshinyCOMPASS
List Shiny DependenciesshinyCOMPASSDeps
Fit the discrete COMPASS ModelSimpleCOMPASS
Subset a COMPASSContainersubset.COMPASSContainer
Summarize a COMPASSContainer Objectsummary.COMPASSContainer
Summarize a COMPASSResult Objectsummary.COMPASSResult
Compute Total Cell CountsTotalCellCounts
Translate marker names to format use by COMPASStranslate_marker_names
Transpose a Listtranspose_list
Generate Unique CombinationsUniqueCombinations UniqueCombinations.COMPASSContainer UniqueCombinations.default