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COMPASS

Combinatorial Polyfunctionality Analysis of Single Cells

COMPASS is now available on Bioconductor!

Getting Started

Install the release version of COMPASS with:

library(BiocInstaller)
biocLite("COMPASS")

or the development version with:

library(BiocInstaller)
useDevel()
biocLite("COMPASS")

To get an idea of how to use COMPASS, read the vignette.

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Version

Version

1.8.0

License

Artistic-2.0

Maintainer

Greg Finak

Last Published

February 15th, 2017

Functions in COMPASS (1.8.0)

COMPASSContainer-data

Simulated COMPASSContainer
plot.COMPASSResult

Plot a COMPASSResult
plot2

Plot a pair of COMPASSResults
COMPASS

Fit the COMPASS Model
COMPASSDescription

Get and Set the Description for the Shiny Application
COMPASSResult-accessors

COMPASSResult Accessors
metadata

Metadata
pheatmap

A function to draw clustered heatmaps.
print.COMPASSContainer

Print a COMPASSContainer Object
print.COMPASSResult

Print a COMPASSResult Object
UniqueCombinations

Generate Unique Combinations
categories

Categories
CellCounts

Compute Number of Cells Positive for Certain Cytokine Combinations
SimpleCOMPASS

Fit the discrete COMPASS Model
TotalCellCounts

Compute Total Cell Counts
subset.COMPASSContainer

Subset a COMPASSContainer
transpose_list

Transpose a List
COMPASSContainer

Generate the Data Object used by COMPASS
COMPASSContainerFromGatingSet

Create a COMPASS Container from a GatingSet
markers

Markers
GetThresholdedIntensities

Extract Thresholded Intensities from a GatingSet
shinyCOMPASS

Start a Shiny Application for Visualizing COMPASS Results
shinyCOMPASSDeps

List Shiny Dependencies
FunctionalityScore

Compute the Functionality Score for each subject fit in a COMPASS model
COMPASSResult-data

Simulated COMPASS fit
PolyfunctionalityScore

Compute the Polyfunctionality Score for each subject fit in a COMPASS model
Posterior

Retrieve Posterior Measures from a COMPASS fit
Combinations

Generate Combinations
COMPASS-package

COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells)
merge.COMPASSContainer

Merge Two COMPASSContainers
melt_

Make a 'Wide' data set 'Long'
summary.COMPASSContainer

Summarize a COMPASSContainer Object
summary.COMPASSResult

Summarize a COMPASSResult Object