{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T12:27:43Z","timestamp":1775564863005,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI146028"],"award-info":[{"award-number":["R01 AI146028"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI138709"],"award-info":[{"award-number":["R01 AI138709"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["F30 AI165112"],"award-info":[{"award-number":["F30 AI165112"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32 AI083203"],"award-info":[{"award-number":["T32 AI083203"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad583","type":"journal-article","created":{"date-parts":[[2023,9,23]],"date-time":"2023-09-23T04:03:27Z","timestamp":1695441807000},"source":"Crossref","is-referenced-by-count":10,"title":["<tt>phippery<\/tt>: a software suite for PhIP-Seq data analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5838-7840","authenticated-orcid":false,"given":"Jared G","family":"Galloway","sequence":"first","affiliation":[{"name":"Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7289-845X","authenticated-orcid":false,"given":"Kevin","family":"Sung","sequence":"additional","affiliation":[{"name":"Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, 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Program, University of Washington , Seattle, WA 98195, USA"}]},{"given":"Zak A","family":"Yaffe","sequence":"additional","affiliation":[{"name":"Human Biology Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, USA"},{"name":"Molecular and Cellular Biology Program, University of Washington , Seattle, WA 98195, USA"},{"name":"Medical Scientist Training Program, University of Washington , Seattle, WA 98195, USA"}]},{"given":"Ryan","family":"Yucha","sequence":"additional","affiliation":[{"name":"Human Biology Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, USA"},{"name":"Department of Microbiology, University of Washington School of Medicine , Seattle, WA 98195, USA"}]},{"given":"Julie","family":"Overbaugh","sequence":"additional","affiliation":[{"name":"Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, USA"},{"name":"Human Biology Division, Fred Hutchinson Cancer Center , Seattle, WA 98109, 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