Chronogram: an R package for data curation and analysis of infection and vaccination cohort studies.

Autor:	Greenwood D; The Francis Crick Institute, London, NW1 1AT, United Kingdom., Shawe-Taylor M; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, W1T 7HA, United Kingdom., Townsley H; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, W1T 7HA, United Kingdom., Gahir J; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, W1T 7HA, United Kingdom., Sahadeo N; Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago., Alhassan Y; Department of Biostatistics, School of Public Health, University of Ghana, Accra, Ghana.; Yemaachi Biotech, Accra, Ghana., Chaloner C; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; UCL Centre for Kidney and Bladder Health, Division of Medicine, Royal Free Hospital, London, NW3 2PF, United Kingdom., Galgut O; Clinical Immunology Service, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, United Kingdom., Kelly G; The Francis Crick Institute, London, NW1 1AT, United Kingdom., Bauer DLV; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), United Kingdom., Wall EC; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, W1T 7HA, United Kingdom.; Research Department of Infection, Division of Infection and Immunity, UCL, London, WC1E 6BT, United Kingdom., Wu MY; COVID Surveillance Unit, The Francis Crick Institute, London, NW1 1AT, United Kingdom., Carr EJ; The Francis Crick Institute, London, NW1 1AT, United Kingdom.; UCL Centre for Kidney and Bladder Health, Division of Medicine, Royal Free Hospital, London, NW3 2PF, United Kingdom.
Jazyk:	angličtina
Zdroj:	Bioinformatics advances [Bioinform Adv] 2024 Sep 27; Vol. 4 (1), pp. vbae146. Date of Electronic Publication: 2024 Sep 27 (Print Publication: 2024).
DOI:	10.1093/bioadv/vbae146
Abstrakt:	Motivation: Observational cohort studies that track vaccine and infection responses offer real-world data to inform pandemic policy. Translating biological hypotheses, such as whether different patterns of accumulated antigenic exposures confer differing antibody responses, into analysis code can be onerous, particularly when source data is dis-aggregated. Results: The R package chronogram introduces the class chronogram, where metadata is seamlessly aggregated with sparse infection episode, clinical and laboratory data. Each experimental modality is added sequentially, allowing the incorporation of new data, such as specialized time-consuming research assays, or their downstream analyses. Source data can be any rectangular data format, including database tables (such as structured query language databases). This supports annotations that aggregate data types/sources, for example, combining symptoms, molecular testing, and sequencing of one or more infectious episodes in a pathogen-agnostic manner. Chronogram arranges observational data to allow the translation of biological hypotheses into their corresponding code via a shared vocabulary. Availability and Implementation: Chronogram is implemented R and available under an MIT licence at: https://www.github.com/FrancisCrickInstitute/chronogram ; a user manual is available at: https://franciscrickinstitute.github.io/chronogram/. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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