To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SamSPECTRAL")

In most cases, you don't need to download the package archive at all.

SamSPECTRAL

 

Identifies cell population in flow cytometry data.

Bioconductor version: Release (3.1)

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 sample. For instructions on manual installation, refer to the PDF file provided in the following documentation.

Author: Habil Zare and Parisa Shooshtari

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

Citation (from within R, enter citation("SamSPECTRAL")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SamSPECTRAL")

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, Software, StemCells
Version 1.22.0
In Bioconductor since BioC 2.6 (R-2.11) (5.5 years)
License GPL (>= 2)
Depends R (>= 2.10)
Imports methods
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Depends On Me
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Build Report  

Package Archives

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

Package Source SamSPECTRAL_1.22.0.tar.gz
Windows Binary SamSPECTRAL_1.22.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SamSPECTRAL_1.22.0.tgz
Mac OS X 10.9 (Mavericks) SamSPECTRAL_1.22.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SamSPECTRAL/tree/release-3.1
Package Short Url http://bioconductor.org/packages/SamSPECTRAL/
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