SamSPECTRAL: Identifies cell population in flow cytometry data.

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.

AuthorHabil Zare and Parisa Shooshtari
Date of publicationNone
MaintainerHabil Zare <zare@txstate.edu>
LicenseGPL (>= 2)
Version1.28.0

View on Bioconductor

Files in this package

SamSPECTRAL/DESCRIPTION
SamSPECTRAL/NAMESPACE
SamSPECTRAL/R
SamSPECTRAL/R/Building_Communities.R SamSPECTRAL/R/Civilized_Spectral_Clustering.R SamSPECTRAL/R/Conductance_Calculation.R SamSPECTRAL/R/Connecting.R SamSPECTRAL/R/SamSPECTRAL.R SamSPECTRAL/R/check.SamSPECTRAL.input.R SamSPECTRAL/R/kneepointDetection.R
SamSPECTRAL/build
SamSPECTRAL/build/vignette.rds
SamSPECTRAL/data
SamSPECTRAL/data/eigen.values.10.RData
SamSPECTRAL/data/eigen.values.1000.RData
SamSPECTRAL/data/small_data.RData
SamSPECTRAL/data/stm.RData
SamSPECTRAL/inst
SamSPECTRAL/inst/CITATION
SamSPECTRAL/inst/doc
SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.R
SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.Rnw
SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.pdf
SamSPECTRAL/man
SamSPECTRAL/man/Building_Communities.Rd SamSPECTRAL/man/Civilized_Spectral_Clustering.Rd SamSPECTRAL/man/Conductance_Calculation.Rd SamSPECTRAL/man/Connecting.Rd SamSPECTRAL/man/SamSPECTRAL-package.Rd SamSPECTRAL/man/SamSPECTRAL.Rd SamSPECTRAL/man/check.SamSPECTRAL.input.Rd SamSPECTRAL/man/eigen.values.10.Rd SamSPECTRAL/man/eigen.values.1000.Rd SamSPECTRAL/man/kneepointDetection.Rd SamSPECTRAL/man/small.Rd SamSPECTRAL/man/stmFSC.Rd
SamSPECTRAL/src
SamSPECTRAL/src/Rinit.c
SamSPECTRAL/src/conductance_computation.c
SamSPECTRAL/src/maximum_of_rows.c
SamSPECTRAL/vignettes
SamSPECTRAL/vignettes/Clustering_by_SamSPECTRAL.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.