SamSPECTRAL

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SamSPECTRAL.

Identifies cell population in flow cytometry data.


Bioconductor version: 3.7

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 txstate.edu>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
A modified spectral clustering method for clustering Flow Cytometry Data PDF R Script
Reference Manual PDF

Details

biocViews Cancer, CellBiology, Clustering, FlowCytometry, HIV, Software, StemCells
Version 1.34.0
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License GPL (>= 2)
Depends R (>= 3.3.3)
Imports methods
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Depends On Me
Imports Me CONFESS, ddPCRclust
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Package Archives

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

Source Package SamSPECTRAL_1.34.0.tar.gz
Windows Binary SamSPECTRAL_1.34.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SamSPECTRAL_1.34.0.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/
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Old Source Packages for BioC 3.7 Source Archive