SamSPECTRAL

DOI: 10.18129/B9.bioc.SamSPECTRAL    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SamSPECTRAL.

Identifies cell population in flow cytometry data.

Bioconductor version: 3.9

Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples.

Author: Habil Zare and Parisa Shooshtari

Maintainer: Habil <zare at u.washington.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SamSPECTRAL")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SamSPECTRAL")

 

PDF	R Script	A modified spectral clustering method for clustering Flow Cytometry Data
PDF		Reference Manual

Details

biocViews	Cancer, CellBiology, Clustering, FlowCytometry, HIV, ImmunoOncology, Software, StemCells
Version	1.38.0
In Bioconductor since	BioC 2.6 (R-2.11) (9.5 years)
License	GPL (>= 2)
Depends	R (>= 3.3.3)
Imports	methods
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	CONFESS, ddPCRclust
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SamSPECTRAL_1.38.0.tar.gz
Windows Binary	SamSPECTRAL_1.38.0.zip
Mac OS X 10.11 (El Capitan)	SamSPECTRAL_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SamSPECTRAL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SamSPECTRAL
Package Short Url	https://bioconductor.org/packages/SamSPECTRAL/
Package Downloads Report	Download Stats