SamSPECTRAL: Identifies cell population in flow cytometry data.

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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
Date of publication
None
Maintainer
Habil Zare <zare@txstate.edu>
License
GPL (>= 2)
Version
1.28.0

View on Bioconductor

Man pages

Building_Communities
Builds the communities from the set of all data points.
check.SamSPECTRAL.input
Checks the input to SamSPECTRAL.
Civilized_Spectral_Clustering
Runs the spectral clustering algorithm on the sample points.
Conductance_Calculation
Computes the conductance between communities.
Connecting
Combines the spectral clusters to build the connected...
eigen.values.10
Eigenvalues for building the SamSPECTRAL vignette.
eigen.values.1000
Eigenvalues for building the SamSPECTRAL vignette.
kneepointDetection
Fits 2 regression lines to data to estimate the knee (or...
SamSPECTRAL
Identifies the cell populations in flow cytometry data.
SamSPECTRAL-package
Identifying cell populations in flow cytometry data.
small
Flow cytometry data to test SamSPECTRAL algorithm.
stmFSC
Flow cytometry data to test SamSPECTRAL algorithm.

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