AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data

MOTIVATION: AliGater is an open-source framework to accelerate the development of bioinformatic pipelines for the analysis of large-scale, high-dimensional flow cytometry data. AliGater provides a Python package for automatic feature extraction workflows, as well as building blocks to construct anal...

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Detalles Bibliográficos
Autores principales: Ekdahl, Ludvig, Arrizabalaga, Antton Lamarca, Ali, Zain, Cafaro, Caterina, de Lapuente Portilla, Aitzkoa Lopez, Nilsson, Björn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Application Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10438955/
https://www.ncbi.nlm.nih.gov/pubmed/37600847
http://dx.doi.org/10.1093/bioadv/vbad103
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author Ekdahl, Ludvig
Arrizabalaga, Antton Lamarca
Ali, Zain
Cafaro, Caterina
de Lapuente Portilla, Aitzkoa Lopez
Nilsson, Björn
author_facet Ekdahl, Ludvig
Arrizabalaga, Antton Lamarca
Ali, Zain
Cafaro, Caterina
de Lapuente Portilla, Aitzkoa Lopez
Nilsson, Björn
author_sort Ekdahl, Ludvig
collection PubMed
description MOTIVATION: AliGater is an open-source framework to accelerate the development of bioinformatic pipelines for the analysis of large-scale, high-dimensional flow cytometry data. AliGater provides a Python package for automatic feature extraction workflows, as well as building blocks to construct analysis pipelines. RESULTS: We illustrate the use of AliGater in a high-resolution flow cytometry-based genome-wide association study on 46 immune cell populations in 14 288 individuals. AVAILABILITY AND IMPLEMENTATION: Source code and documentation at https://github.com/LudvigEk/aligater and https://aligater.readthedocs.io
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spelling pubmed-104389552023-08-19 AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data Ekdahl, Ludvig Arrizabalaga, Antton Lamarca Ali, Zain Cafaro, Caterina de Lapuente Portilla, Aitzkoa Lopez Nilsson, Björn Bioinform Adv Application Note MOTIVATION: AliGater is an open-source framework to accelerate the development of bioinformatic pipelines for the analysis of large-scale, high-dimensional flow cytometry data. AliGater provides a Python package for automatic feature extraction workflows, as well as building blocks to construct analysis pipelines. RESULTS: We illustrate the use of AliGater in a high-resolution flow cytometry-based genome-wide association study on 46 immune cell populations in 14 288 individuals. AVAILABILITY AND IMPLEMENTATION: Source code and documentation at https://github.com/LudvigEk/aligater and https://aligater.readthedocs.io Oxford University Press 2023-08-04 /pmc/articles/PMC10438955/ /pubmed/37600847 http://dx.doi.org/10.1093/bioadv/vbad103 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Application Note
Ekdahl, Ludvig
Arrizabalaga, Antton Lamarca
Ali, Zain
Cafaro, Caterina
de Lapuente Portilla, Aitzkoa Lopez
Nilsson, Björn
AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title_full AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title_fullStr AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title_full_unstemmed AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title_short AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
title_sort aligater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data
topic Application Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10438955/
https://www.ncbi.nlm.nih.gov/pubmed/37600847
http://dx.doi.org/10.1093/bioadv/vbad103
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