PAC: Partition-Assisted Clustering

Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering. The package also provides functions for effectively visualizing the clustering results. It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.

Author
Dangna Li, Henry Li
Date of publication
2016-04-10 16:25:22
Maintainer
Dangna Li <ldangna@gmail.com>
License
GPL-3
Version
1.0.5

View on CRAN

Man pages

aggregateData
Aggregates results from the clustering and merging step.
BSPLeaveCenter
Finds N Leaf centers in the data
clusterNames
Get the top features that differentiate the clusters based on...
clusterPropHeatmap
Make heatmap illustrating the cluster proportions across...
filteredResults_JSON
Obtain the input to zoomable packed circles plot. The...
fmeasure
Compute the F measure between the ground truth and the...
makeList
Helper function to obtain a JSON-friendly format of a matrix...
PAC
PAC (Partition Assisted Clustering)
packedCircleInput
Make packed circles plot illustrating the cluster proportions...
signalLevelHeatmap
Make heatmap illustrating the signel levels for clusters. For...

Files in this package

PAC
PAC/inst
PAC/inst/doc
PAC/inst/doc/intro.html
PAC/inst/doc/intro.R
PAC/inst/doc/intro.Rmd
PAC/src
PAC/src/Makevars
PAC/src/bsp.h
PAC/src/util.cc
PAC/src/pac-wrapper.cc
PAC/src/util.h
PAC/src/bspconst.h
PAC/src/bsp.cc
PAC/src/RcppExports.cpp
PAC/src/type.h
PAC/NAMESPACE
PAC/R
PAC/R/PAC.R
PAC/R/makeList.R
PAC/R/signalLevelHeatmap.R
PAC/R/filteredResults_JSON.R
PAC/R/aggregateData.R
PAC/R/RcppExports.R
PAC/R/packedCircleInput.R
PAC/R/clusterPropHeatmap.R
PAC/R/fmeasure.R
PAC/R/clusterNames.R
PAC/vignettes
PAC/vignettes/CyTOFData.txt
PAC/vignettes/subpop_names_top2.txt
PAC/vignettes/intro.Rmd
PAC/vignettes/references.bib
PAC/vignettes/bioexample.html
PAC/vignettes/zoomablePackedCirclesInput.txt
PAC/vignettes/bioexample.Rmd
PAC/MD5
PAC/build
PAC/build/vignette.rds
PAC/DESCRIPTION
PAC/man
PAC/man/PAC.Rd
PAC/man/clusterNames.Rd
PAC/man/BSPLeaveCenter.Rd
PAC/man/clusterPropHeatmap.Rd
PAC/man/makeList.Rd
PAC/man/packedCircleInput.Rd
PAC/man/fmeasure.Rd
PAC/man/signalLevelHeatmap.Rd
PAC/man/filteredResults_JSON.Rd
PAC/man/aggregateData.Rd
PAC/configure.win
PAC/cleanup.win