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For instance, colorectal cancers (CRCs) can be classified into four CRC consensus molecular subgroups (CMS) or five intrinsic (CRIS) sub-types that have prognostic and predictive value. Breast cancer (BRCA) has five PAM50 molecular subgroups with similar value, and the OncotypeDX test provides transcriptomic based clinically actionable treatment-risk stratification. However, assigning samples to these subtypes and other transcriptionally inferred predictions is time consuming and requires significant bioinformatics experience. There is no \"universal\" method of using data from diverse assay\/sequencing platforms to provide subgroup classification using the established classifier sets of genes (CMS, CRIS, PAM50, OncotypeDX), nor one which in provides additional useful functional annotations such as cellular composition, single-sample Gene Set Enrichment Analysis, or prediction of transcription factor activity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address this bottleneck, we developed classifieR, an easy-to-use R-Shiny based web application that supports flexible rapid single sample annotation of transcriptional profiles derived from cancer patient samples form diverse platforms. We demonstrate the utility of the \" classifieR\" framework to applications focused on the analysis of transcriptional profiles from colorectal (classifieRc) and breast (classifieRb). Samples are annotated with disease relevant transcriptional subgroups (CMS\/CRIS sub-types in classifieRc and PAM50\/inferred OncotypeDX in classifieRb), estimation of cellular composition using MCP-counter and xCell, single-sample Gene Set Enrichment Analysis (ssGSEA) and transcription factor activity predictions with Discriminant Regulon Expression Analysis (DoRothEA).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>classifieR provides a framework which enables labs without access to a dedicated bioinformation can get information on the molecular makeup of their samples, providing an insight into patient prognosis, druggability and also as a tool for analysis and discovery. Applications are hosted online at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/generatr.qub.ac.uk\/app\/classifieRc\">https:\/\/generatr.qub.ac.uk\/app\/classifieRc<\/jats:ext-link>and<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/generatr.qub.ac.uk\/app\/classifieRb\">https:\/\/generatr.qub.ac.uk\/app\/classifieRb<\/jats:ext-link>after signing up for an account on<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/generatr.qub.ac.uk\">https:\/\/generatr.qub.ac.uk<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-022-04641-x","type":"journal-article","created":{"date-parts":[[2022,3,31]],"date-time":"2022-03-31T13:21:48Z","timestamp":1648732908000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes"],"prefix":"10.1186","volume":"23","author":[{"given":"Gerard P.","family":"Quinn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamas","family":"Sessler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baharak","family":"Ahmaderaghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shauna","family":"Lambe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harper","family":"VanSteenhouse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Lawler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Wappett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce","family":"Seligmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel B.","family":"Longley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon S.","family":"McDade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,3,31]]},"reference":[{"key":"4641_CR1","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1038\/nm.3967","volume":"21","author":"J Guinney","year":"2015","unstructured":"Guinney J, Dienstmann R, Wang X, de Reyni\u00e8s A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350\u20136.","journal-title":"Nat Med"},{"key":"4641_CR2","doi-asserted-by":"publisher","first-page":"15107","DOI":"10.1038\/ncomms15107","volume":"8","author":"C Isella","year":"2017","unstructured":"Isella C, Brundu F, Bellomo SE, Galimi F, Zanella E, Porporato R, Petti C, Fiori A, Orzan F, Senetta R, et al. Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. Nat Commun. 2017;8:15107.","journal-title":"Nat Commun"},{"key":"4641_CR3","doi-asserted-by":"publisher","first-page":"15657","DOI":"10.1038\/ncomms15657","volume":"8","author":"PD Dunne","year":"2017","unstructured":"Dunne PD, Alderdice M, O\u2019Reilly PG, Roddy AC, McCorry AMB, Richman S, Maughan T, McDade SS, Johnston PG, Longley DB, et al. Cancer-cell intrinsic gene expression signatures overcome intratumoural heterogeneity bias in colorectal cancer patient classification. Nat Commun. 2017;8:15657.","journal-title":"Nat Commun"},{"key":"4641_CR4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1200\/PO.17.00241","volume":"2","author":"WL Allen","year":"2018","unstructured":"Allen WL, et al. Transcriptional subtyping and CD8 immunohistochemistry identifies patients with stage II and III colorectal cancer with poor prognosis who benefit from adjuvant chemotherapy. JCO Precis Oncol. 2018;2:1\u201315.","journal-title":"JCO Precis Oncol"},{"issue":"2","key":"4641_CR5","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s11894-019-0674-9","volume":"21","author":"DG Menter","year":"2019","unstructured":"Menter DG, et al. Back to the colorectal cancer consensus molecular subtype future. 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