chickn: chickn-package
In chickn: 'Compressive' Hierarchical Kernel Clustering Toolbox
Description
Author(s)
References
Description
The R package chickn implements the Chromatogram Hierarchical Compressive K-means with Nystrom approximation
clustering approach. It is designed to cluster a large collection of high-resolution
mass spectrometry signals (chromatographic profiles) relying on a compressed version of the data (a.k.a. data sketch).
Data compression is achieved following the guidelines for Nystrom approximation provided by \insertCitewang2019scalablechickn
and the sketching operator from \insertCiteDBLP:journals/corr/KerivenBGP16chickn.
The Filebacked Big Matrix (FBM) class from the bigstatsr package
is used to store and to manupulate matrices, which cannot be load in memory.
Author(s)
Olga Permiakova, Romain Guibert, Thomas Burger
References
Permiakova O, Guibert R, Kraut A, Fortin T, Hesse AM, Burger T (2020) "CHICKN: Extraction of peptide chromatographic
elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis."
BMC Bioinformatics (under revision).
chickn documentation built on Jan. 13, 2021, 10:53 p.m.
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Description Author(s) References
Description
The R package chickn implements the Chromatogram Hierarchical Compressive K-means with Nystrom approximation
clustering approach. It is designed to cluster a large collection of high-resolution
mass spectrometry signals (chromatographic profiles) relying on a compressed version of the data (a.k.a. data sketch).
Data compression is achieved following the guidelines for Nystrom approximation provided by \insertCitewang2019scalablechickn
and the sketching operator from \insertCiteDBLP:journals/corr/KerivenBGP16chickn.
The Filebacked Big Matrix (FBM) class from the bigstatsr package
is used to store and to manupulate matrices, which cannot be load in memory.
Author(s)
Olga Permiakova, Romain Guibert, Thomas Burger
References
Permiakova O, Guibert R, Kraut A, Fortin T, Hesse AM, Burger T (2020) "CHICKN: Extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis." BMC Bioinformatics (under revision).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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