SamSPECTRAL
- Spectral clustering cannot be directly applied to large datasets such as flow cytometry data due to time and memory limitations. This issue can be addressed by performing a delicate data reduction that is designed specifically for spectral clustering.
- SamSPECTRAL is the R package that identifies cell populations in flow cytometry data.
It implements an enhancement to spectral clustering technique and can therefore be applied to large data sets including flow cytometry data.
- Prerequisites: A computer with a Linux-based operating system, make, gcc compiler and R 2.0.0 or later.
- Please visit SamSPECTRAL at BioConductor (> 2.6)
to download and install the latest SamSPECTRAL package or to obtain the User's manual.
- If your R version is 2.11 or newer, the easiest way to install SamSPECTRAL is from BioConductor 2.6 or later by typing the following in R
source("http://bioconductor.org/biocLite.R")
biocLite("SamSPECTRAL")
- You can install SamSPECTRAL manually from sources if your R version is less than 2.11. Download the SamSPECTRAL_x.y.z.tar.gz file from
BioConductor and type the following to install the package manually
R CMD INSTALL SamSPECTRAL_x.y.z.tar.gz including full path to the file
(Replace x.y.z to match the downloaded version of SamSPECTRAL)
- Reference:
Zare, H. and Shooshtari, P. and Gupta, A. and Brinkman R.B: Data reduction for spectral clustering to
analyze high throughput flow cytometry data. BMC Bioinformatics 2010,11:403.
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