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phippery: a software suite for PhIP-Seq data analysis.
Galloway, Jared G; Sung, Kevin; Minot, Samuel S; Garrett, Meghan E; Stoddard, Caitlin I; Willcox, Alexandra C; Yaffe, Zak A; Yucha, Ryan; Overbaugh, Julie; Matsen, Frederick A.
Afiliación
  • Galloway JG; Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Sung K; Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Minot SS; Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Garrett ME; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Stoddard CI; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
  • Willcox AC; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Yaffe ZA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • Yucha R; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
  • Overbaugh J; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.
  • Matsen FA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Bioinformatics ; 39(10)2023 10 03.
Article en En | MEDLINE | ID: mdl-37740324
SUMMARY: We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. AVAILABILITY AND IMPLEMENTATION: All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Imidazoles Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Imidazoles Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido