{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T01:39:25Z","timestamp":1782783565927,"version":"3.54.5"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming.<\/jats:p>\n                  <jats:p>Availability and implementation: destiny is an open-source R\/Bioconductor package \u201cbioconductor.org\/packages\/destiny\u201d also available at www.helmholtz-muenchen.de\/icb\/destiny. A detailed vignette describing functions and workflows is provided with the package.<\/jats:p>\n                  <jats:p>Contact: \u00a0carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv715","type":"journal-article","created":{"date-parts":[[2015,12,14]],"date-time":"2015-12-14T21:54:41Z","timestamp":1450130081000},"page":"1241-1243","source":"Crossref","is-referenced-by-count":663,"title":["<i>destiny<\/i>\n                    : diffusion maps for large-scale single-cell data in R"],"prefix":"10.1093","volume":"32","author":[{"given":"Philipp","family":"Angerer","sequence":"first","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laleh","family":"Haghverdi","sequence":"additional","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maren","family":"B\u00fcttner","sequence":"additional","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian J.","family":"Theis","sequence":"additional","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"},{"name":"2 Technische Universit\u00e4t M\u00fcnchen, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Boltzmannstr. 3, 85748 Garching, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carsten","family":"Marr","sequence":"additional","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Buettner","sequence":"additional","affiliation":[{"name":"1 Helmholtz Zentrum M\u00fcnchen - German Research Center for Environmental Health, Institute of Computational Biology, Ingolst\u00e4dter Landstr. 1, 85764 Neuherberg, Germany and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,12,14]]},"reference":[{"key":"2023020112211254000_btv715-B1","doi-asserted-by":"crossref","first-page":"i626","DOI":"10.1093\/bioinformatics\/bts385","article-title":"A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst","volume":"28","author":"Buettner","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112211254000_btv715-B2","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1137\/070696325","article-title":"Diffusion maps, reduction coordinates, and low dimensional representation of stochastic systems","volume":"7","author":"Coifman","year":"2008","journal-title":"Multisc. 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