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SamSPECTRAL specifications

Information


Unique identifier OMICS_05638
Name SamSPECTRAL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.34.0
Stability Stable
Requirements
methods, R(>=3.3.3)
Maintained Yes

Versioning


No version available

Documentation


Publication for SamSPECTRAL

SamSPECTRAL citations

 (8)
library_books

Immunophenotype Discovery, Hierarchical Organization, and Template Based Classification of Flow Cytometry Samples

2016
PMCID: 5005935
PMID: 27630823
DOI: 10.3389/fonc.2016.00188

[…] high-dimensional or high-throughput FC data. To address the gating problem, researchers have proposed several automated clustering algorithms, such as FLAME (), FLOCK (), flowClust (), flowMeans (), SamSPECTRAL (), SWIFT (), etc. Aghaeepour et al. () provides a state-of-the-art summary of the field.Different algorithms perform better for different FC datasets as was observed in a set of challenge […]

library_books

Single and multi subject clustering of flow cytometry data for cell type identification and anomaly detection

2016
BMC Med Genomics
PMCID: 4980779
PMID: 27510222
DOI: 10.1186/s12920-016-0201-x

[…] n surface markers. The staining panel contains antibodies to surface markers and intracellular proteins.Additionally, we compared our method against four well-known algorithms in the field: FLAME [], SamSpectral [], flowMerge [], and flowMeans []. […]

library_books

Multidimensional Clusters of CD4+ T Cell Dysfunction Are Primarily Associated with the CD4/CD8 Ratio in Chronic HIV Infection

2015
PLoS One
PMCID: 4581870
PMID: 26402620
DOI: 10.1371/journal.pone.0137635

[…] aussian models, t-mixture models and skew-t models []. These methods show robustness that follows predefined models, but they might be slow at estimating model parameters of high-dimensional dataset. SamSPECTRAL [] is an example of the graph-based methods, while multidimensional clustering approaches available include SPADE [], flowMeans [] and FLOCK []. Here, we investigated whether one of the ex […]

library_books

An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation

2015
Front Immunol
PMCID: 4515551
PMID: 26284066
DOI: 10.3389/fimmu.2015.00380

[…] -user were used as guidance, the f-scores improved dramatically, with five algorithms ending up with scores of 0.90 or greater. As before, this not only included ADIcyt, FlowMeans, and FLOCK but also SamSpectral () and TCLUST (). The overall conclusion from this challenge was that although some packages performed better than others, most performed well and this was largely dependent on the dataset […]

call_split

Flow Cytometry Bioinformatics

2013
PLoS Comput Biol
PMCID: 3867282
PMID: 24363631
DOI: 10.1371/journal.pcbi.1003365
call_split See protocol

[…] al clustering approaches have recently been developed, including model-based algorithms (e.g., flowClust and FLAME ), density-based algorithms (e.g., FLOCK and SWIFT), graph-based approaches (e.g., SamSPECTRAL ), and, most recently, hybrids of several approaches (flowMeans and flowPeaks ). These algorithms are different in terms of memory and time complexity, their software requirements, their […]

library_books

Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis

2013
BMC Genomics
PMCID: 3549810
PMID: 23369194
DOI: 10.1186/1471-2164-14-S1-S14

[…] ectly apply classical spectral clustering [-] to the lymphoma data because it involved computing eigenvectors of a big n-by-n matrix where n ranges from 20,000 to 70,000. Instead, we have made use of SamSPECTRAL that is our enhanced spectral clustering method capable of analyzing large amount of data in a reasonable amount of time; it has also a good memory footprints [].SamSPECTRAL performs a spe […]

Citations

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SamSPECTRAL institution(s)
Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada

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