{"doi":"10.1093/bioinformatics/btad583","title":"<tt>phippery</tt>: a software suite for PhIP-Seq data analysis","abstract":"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.","journal":"Bioinformatics","year":2023,"id":330584,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9573,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":658273,"name":"Kevin Sung","orcid":"0000-0002-7289-845X","position":1,"is_corresponding":false},{"id":433550,"name":"Samuel S. Minot","orcid":"0000-0003-1639-3905","position":2,"is_corresponding":false},{"id":439661,"name":"Meghan Garrett","orcid":"0000-0002-3284-3307","position":3,"is_corresponding":false},{"id":257934,"name":"Caitlin I. Stoddard","orcid":"0000-0002-2750-3228","position":4,"is_corresponding":false},{"id":307694,"name":"Alexandra C. Willcox","orcid":"0000-0001-6037-6841","position":5,"is_corresponding":false},{"id":708682,"name":"Zak A. Yaffe","orcid":"0000-0003-2998-0172","position":6,"is_corresponding":false},{"id":1054797,"name":"Ryan Yucha","orcid":"0009-0000-6009-7041","position":7,"is_corresponding":false},{"id":344987,"name":"Julie Overbaugh","orcid":"0000-0002-0239-9444","position":8,"is_corresponding":false},{"id":72067,"name":"Frederick A. Matsen","orcid":"0000-0003-0607-6025","position":9,"is_corresponding":false},{"id":237899,"name":"Jared Galloway","orcid":"0000-0001-5838-7840","position":0,"is_corresponding":true}],"reference_count":14,"raw_metadata":null,"created_at":"2026-07-19T01:09:14.691473Z","pmid":"37740324","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}