phippery : a software suite for PhIP-Seq data analysis
© The Author(s) 2023. Published by Oxford University Press..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:39 |
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| Enthalten in: |
Bioinformatics (Oxford, England) - 39(2023), 10 vom: 03. Okt. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Galloway, Jared G [VerfasserIn] |
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| Links: |
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| Themen: |
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine |
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| Anmerkungen: |
Date Completed 05.10.2023 Date Revised 10.02.2024 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/bioinformatics/btad583 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM362368295 |
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| 100 | 1 | |a Galloway, Jared G |e verfasserin |4 aut | |
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| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © The Author(s) 2023. Published by Oxford University Press. | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Research Support, N.I.H., Extramural | |
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| 700 | 1 | |a Sung, Kevin |e verfasserin |4 aut | |
| 700 | 1 | |a Minot, Samuel S |e verfasserin |4 aut | |
| 700 | 1 | |a Garrett, Meghan E |e verfasserin |4 aut | |
| 700 | 1 | |a Stoddard, Caitlin I |e verfasserin |4 aut | |
| 700 | 1 | |a Willcox, Alexandra C |e verfasserin |4 aut | |
| 700 | 1 | |a Yaffe, Zak A |e verfasserin |4 aut | |
| 700 | 1 | |a Yucha, Ryan |e verfasserin |4 aut | |
| 700 | 1 | |a Overbaugh, Julie |e verfasserin |4 aut | |
| 700 | 1 | |a Matsen, Frederick A |e verfasserin |4 aut | |
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