SamSPECTRAL

Identifies cell population in flow cytometry data.

Bioconductor version: 2.8

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 <hzare at bccrc.ca>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("SamSPECTRAL")

Documentation

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

Details

biocViews Bioinformatics, FlowCytometry, CellBiology, Clustering, Cancer, FlowCytData, StemCells, HIV
Depends R (>= 2.0.0)
Imports methods
Suggests
System Requirements
License GPL version 2 or newer
URL
Depends On Me
Imports Me
Suggests Me
Version 1.6.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source SamSPECTRAL_1.6.0.tar.gz
Windows Binary SamSPECTRAL_1.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary SamSPECTRAL_1.6.0.tgz
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Fred Hutchinson Cancer Research Center