AliGater: a Framework for the Development of Bioinformatic Pipelines for Large-scale, High-dimensional Cytometry Data

Overview

Journal Bioinform Adv

Publisher Oxford University Press

Specialty Biology

Date 2023 Aug 21

PMID 37600847

Authors

Ludvig Ekdahl

Antton Lamarca Arrizabalaga

Zain Ali

Caterina Cafaro

Aitzkoa Lopez de Lapuente Portilla

Bjorn Nilsson

Affiliations

Soon will be listed here.

Abstract

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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