SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples.

Algorithms Humans Mutation Neoplasms / diagnosis
Bioinformatics Cancer Genomics

Journal

STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501

Informations de publication

Date de publication:
16 09 2022
Historique:
received: 01 04 2022
revised: 12 05 2022
accepted: 08 06 2022
pubmed: 3 7 2022
medline: 23 9 2022
entrez: 2 7 2022
Statut: ppublish

Résumé

We outline the features of the R package SparseSignatures and its application to determine the signatures contributing to mutation profiles of tumor samples. We describe installation details and illustrate a step-by-step approach to (1) prepare the data for signature analysis, (2) determine the optimal parameters, and (3) employ them to determine the signatures and related exposure levels in the point mutation dataset. For complete details on the use and execution of this protocol, please refer to Lal et al. (2021).

Identifiants

DOI: 10.1016/j.xpro.2022.101513 PMID: 35779264 PMC: PMC9256827
pubmed: 35779264
pii: S2666-1667(22)00393-8
doi: 10.1016/j.xpro.2022.101513
pmc: PMC9256827
pii:
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

101513

Informations de copyright

Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests A.L. is an employee of Insitro, South San Francisco, CA, USA. Insitro had no involvement in this work.

Auteurs

Lorenzo Mella (L)

Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.

Avantika Lal (A)

Insitro, 279 E Grand Avenue, South San Francisco, CA, USA.

Fabrizio Angaroni (F)

Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy.

Davide Maspero (D)

Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy.

Rocco Piazza (R)

Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Milan, Italy; Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, Milan, Italy.

Arend Sidow (A)

Department of Pathology, Stanford University, Stanford, CA, USA.

Marco Antoniotti (M)

Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy; Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, Milan, Italy. Electronic address: marco.antoniotti@unimib.it.

Alex Graudenzi (A)

Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy; Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, Milan, Italy; Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Segrate, Italy. Electronic address: alex.graudenzi@unimib.it.

Daniele Ramazzotti (D)

Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Milan, Italy. Electronic address: daniele.ramazzotti@unimib.it.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › SparseSignatures: An R package using...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › SparseSignatures: An R package using...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › SparseSignatures: An R package using...
questionsmedicales.fr › Tumeurs › SparseSignatures: An R package using...