ArticleBioinformatics (Oxford, England)2023
phippery: a software suite for PhIP-Seq data analysis.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
8 citing papers in PubMed, 8 citations in OpenAlex.
- Assessing VirScan serosurvey epitope profiling variability between in-clinic venous blood draw and capillary blood self-sampling device.Microbiology spectrum · 2026Article
- Influence of B cell-lineage targeted CAR-T cell therapy on humoral immunity and vaccine-induced antibody response.Nature communications · 2026Article
- Article
- PhIP-Seq: unveiling the complexity of antibody repertoires in health and disease.Frontiers in immunology · 2026Review
- Genetic and environmental imprints on T cell receptor repertoires as predictors of graft-versus-host disease.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive phage display viral antibody profiling using VirScan: potential applications in chronic immune-mediated disease.Journal of virology · 2024Review
- The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2.PLoS pathogens · 2024Article
- PhIP-Seq: methods, applications and challenges.Frontiers in bioinformatics · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
summaryWe 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.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.