{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T16:26:15Z","timestamp":1764174375316},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T00:00:00Z","timestamp":1493856000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet (Single Cell Heterogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using Shannon Profile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the Profile of Shannon Difference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and\/or within cell populations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http:\/\/labpages2.moffitt.org\/chen\/software\/.<\/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\/btx297","type":"journal-article","created":{"date-parts":[[2017,5,3]],"date-time":"2017-05-03T19:11:11Z","timestamp":1493838671000},"page":"2951-2953","source":"Crossref","is-referenced-by-count":12,"title":["SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer"],"prefix":"10.1093","volume":"33","author":[{"given":"Jiannong","family":"Li","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inna","family":"Smalley","sequence":"additional","affiliation":[{"name":"Departments of Tumor Biology and Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J","family":"Schell","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keiran S M","family":"Smalley","sequence":"additional","affiliation":[{"name":"Departments of Tumor Biology and Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y Ann","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,5,4]]},"reference":[{"key":"2023020206395732700_btx297-B1","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nbt.2594","article-title":"viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia","volume":"31","author":"Amir el","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023020206395732700_btx297-B2","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1038\/nprot.2016.066","article-title":"Visualization and cellular hierarchy inference of single-cell data using SPADE","volume":"11","author":"Anchang","year":"2016","journal-title":"Nat. Protocols"},{"key":"2023020206395732700_btx297-B3","doi-asserted-by":"crossref","first-page":"e54170","DOI":"10.1371\/journal.pone.0054170","article-title":"Detection and clinical significance of intratumoral EGFR mutational heterogeneity in Chinese patients with advanced non-small cell lung cancer","volume":"8","author":"Bai","year":"2013","journal-title":"PloS One"},{"key":"2023020206395732700_btx297-B4","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nmeth.3961","article-title":"Single-cell multimodal profiling reveals cellular epigenetic heterogeneity","volume":"13","author":"Cheow","year":"2016","journal-title":"Nat. Methods"},{"key":"2023020206395732700_btx297-B5","first-page":"1","article-title":"Multivariate adaptive regression splines","author":"Friedman","year":"1991","journal-title":"Ann. Statis"},{"year":"2010","author":"Hernandez-Walls","key":"2023020206395732700_btx297-B6"},{"year":"2016","author":"Jekabsons","key":"2023020206395732700_btx297-B7"},{"key":"2023020206395732700_btx297-B8","doi-asserted-by":"crossref","first-page":"e117","DOI":"10.1093\/nar\/gkw430","article-title":"TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis","volume":"44","author":"Ji","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020206395732700_btx297-B9","first-page":"105","article-title":"Tumor heterogeneity: causes and consequences","volume":"1805","author":"Marusyk","year":"2010","journal-title":"Biochim. Et Biophys. Acta"},{"key":"2023020206395732700_btx297-B10","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1038\/leu.2015.361","article-title":"Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors","volume":"30","author":"Mitra","year":"2016","journal-title":"Leukemia"},{"key":"2023020206395732700_btx297-B11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.2307\/1217208","article-title":"The comparison of dendrograms by objective methods","volume":"11","author":"Sokal","year":"1962","journal-title":"Taxon"},{"volume-title":"Ecological Methods","year":"2000","author":"Southwood","key":"2023020206395732700_btx297-B12"},{"key":"2023020206395732700_btx297-B13","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2951\/49040710\/bioinformatics_33_18_2951.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2951\/49040710\/bioinformatics_33_18_2951.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:40:18Z","timestamp":1675320018000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/18\/2951\/3796393"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,5,4]]},"references-count":13,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2017,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx297","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,9,15]]},"published":{"date-parts":[[2017,5,4]]}}}