{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:11Z","timestamp":1772138051785,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T00:00:00Z","timestamp":1654041600000},"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":["1U54AG075936-01"],"award-info":[{"award-number":["1U54AG075936-01"]}],"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":["1K99HG011468"],"award-info":[{"award-number":["1K99HG011468"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>In the exploratory data analysis of single-cell or spatial genomic data, single-cells or spatial spots are often visualized using a two-dimensional plot where cell clusters or spot clusters are marked with different colors. With tens of clusters, current visualization methods often assign visually similar colors to spatially neighboring clusters, making it hard to identify the distinction between clusters. To address this issue, we developed Palo that optimizes the color palette assignment for single-cell and spatial data in a spatially aware manner. Palo identifies pairs of clusters that are spatially neighboring to each other and assigns visually distinct colors to those neighboring pairs. We demonstrate that Palo leads to improved visualization in real single-cell and spatial genomic datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Palo R package is freely available at Github (https:\/\/github.com\/Winnie09\/Palo) and Zenodo (https:\/\/doi.org\/10.5281\/zenodo.6562505).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac368","type":"journal-article","created":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T08:13:38Z","timestamp":1654071218000},"page":"3654-3656","source":"Crossref","is-referenced-by-count":8,"title":["Palo: spatially aware color palette optimization for single-cell and spatial data"],"prefix":"10.1093","volume":"38","author":[{"given":"Wenpin","family":"Hou","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health , Baltimore, MD 21205, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9457-4704","authenticated-orcid":false,"given":"Zhicheng","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine , Durham, NC 27710, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,6,1]]},"reference":[{"key":"2023041405363356400_","article-title":"10X Visium spatial transcriptomics data of mouse anterior brain","year":"2020"},{"key":"2023041405363356400_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1795-z","article-title":"A comparison of automatic cell identification methods for single-cell RNA sequencing data","volume":"20","author":"Abdelaal","year":"2019","journal-title":"Genome Biol"},{"key":"2023041405363356400_","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2019","journal-title":"Nat. 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