SamSPECTRAL
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SamSPECTRAL.
Identifies cell population in flow cytometry data.
Bioconductor version: 3.9
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. See the vignette for more details on how to use this package, some illustrations, and simple examples.
Author: Habil Zare and Parisa Shooshtari
Maintainer: Habil <zare at u.washington.edu>
citation("SamSPECTRAL")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Cancer, CellBiology, Clustering, FlowCytometry, HIV, ImmunoOncology, Software, StemCells |
| Version | 1.38.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3.3) |
| Imports | methods |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | CONFESS, ddPCRclust |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SamSPECTRAL_1.38.0.tar.gz |
| Windows Binary | SamSPECTRAL_1.38.0.zip |
| Mac OS X 10.11 (El Capitan) | SamSPECTRAL_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SamSPECTRAL |
| Source Repository (Developer Access) | git clone [email protected]:packages/SamSPECTRAL |
| Bioc Package Browser | https://code.bioconductor.org/browse/SamSPECTRAL/ |
| Package Short Url | https://bioconductor.org/packages/SamSPECTRAL/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |