{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T02:35:55Z","timestamp":1772591755882,"version":"3.50.1"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,5,28]],"date-time":"2015-05-28T00:00:00Z","timestamp":1432771200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0613-1","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T18:00:48Z","timestamp":1434650448000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":212,"title":["tcR: an R package for T cell receptor repertoire advanced data analysis"],"prefix":"10.1186","volume":"16","author":[{"given":"Vadim I.","family":"Nazarov","sequence":"first","affiliation":[]},{"given":"Mikhail V.","family":"Pogorelyy","sequence":"additional","affiliation":[]},{"given":"Ekaterina A.","family":"Komech","sequence":"additional","affiliation":[]},{"given":"Ivan V.","family":"Zvyagin","sequence":"additional","affiliation":[]},{"given":"Dmitry A.","family":"Bolotin","sequence":"additional","affiliation":[]},{"given":"Mikhail","family":"Shugay","sequence":"additional","affiliation":[]},{"given":"Dmitry M.","family":"Chudakov","sequence":"additional","affiliation":[]},{"given":"Yury B.","family":"Lebedev","sequence":"additional","affiliation":[]},{"given":"Ilgar Z.","family":"Mamedov","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,5,28]]},"reference":[{"key":"613_CR1","doi-asserted-by":"publisher","first-page":"16161","DOI":"10.1073\/pnas.1212755109","volume":"109","author":"A Murugan","year":"2012","unstructured":"Murugan A, Mora T, Walczak AM, Callan CG. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci U S A. 2012;109:16161\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"613_CR2","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/334395a0","volume":"334","author":"M Davis","year":"1988","unstructured":"Davis M, Bjorkman P. T-cell antigen receptor genes and T-cell recognition. Nature. 1988;334:395\u2013402.","journal-title":"Nature"},{"key":"613_CR3","unstructured":"Lefranc M-P, Lefranc G. The T Cell Receptor FactsBook. Gulf Professional Publishing; 2001."},{"key":"613_CR4","doi-asserted-by":"crossref","unstructured":"Lefranc M-P. Immunoglobulin and T Cell Receptor Genes: IMGT and the Birth and Rise of Immunoinformatics. Front Immunol. 2014;5:22.","DOI":"10.3389\/fimmu.2014.00022"},{"key":"613_CR5","doi-asserted-by":"publisher","first-page":"2689","DOI":"10.4049\/jimmunol.1302064","volume":"192","author":"OV Britanova","year":"2014","unstructured":"Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, et al. Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling. J Immunol. 2014;192:2689\u201398.","journal-title":"J Immunol"},{"key":"613_CR6","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1002\/emmm.201100129","volume":"3","author":"IZ Mamedov","year":"2011","unstructured":"Mamedov IZ, Britanova OV, Bolotin DA, Chkalina AV, Staroverov DB, Zvyagin IV, et al. Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBO Mol Med. 2011;3:201\u20137.","journal-title":"EMBO Mol Med"},{"key":"613_CR7","doi-asserted-by":"publisher","first-page":"171ra19","DOI":"10.1126\/scitranslmed.3004794","volume":"5","author":"N Jiang","year":"2013","unstructured":"Jiang N, He J, Weinstein JA, Penland L, Sasaki S, He X-S, et al. Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med. 2013;5:171ra19.","journal-title":"Sci Transl Med"},{"key":"613_CR8","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.4049\/jimmunol.1003898","volume":"186","author":"V Venturi","year":"2011","unstructured":"Venturi V, Quigley MF, Greenaway HY, Ng PC, Ende ZS, McIntosh T, et al. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J Immunol. 2011;186:4285\u201394.","journal-title":"J Immunol"},{"key":"613_CR9","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1073\/pnas.0913939107","volume":"107","author":"C Wang","year":"2010","unstructured":"Wang C, Sanders CM, Yang Q, Schroeder HW, Wang E, Babrzadeh F, et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A. 2010;107:1518\u201323.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"613_CR10","first-page":"26","volume":"8","author":"E Alamyar","year":"2012","unstructured":"Alamyar E, Giudicelli V, Li S, Duroux P, Lefranc M-P. IMGT\/HighV-QUEST: the IMGT web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res. 2012;8:26.","journal-title":"Immunome Res"},{"key":"613_CR11","doi-asserted-by":"crossref","unstructured":"Alamyar E, Duroux P, Lefranc M-P, Giudicelli V. IMGT tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT\/V-QUEST and IMGT\/HighV-QUEST for NGS. Methods Mol Biol. 2012;569\u2013604.","DOI":"10.1007\/978-1-61779-842-9_32"},{"issue":"May","key":"613_CR12","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1038\/ncomms3333","volume":"4","author":"S Li","year":"2013","unstructured":"Li S, Lefranc M-P, Miles JJ, Alamyar E, Giudicelli V, Duroux P, et al. IMGT\/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun. 2013;4(May):2333.","journal-title":"Nat Commun"},{"key":"613_CR13","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1038\/nmeth.2555","volume":"10","author":"DA Bolotin","year":"2013","unstructured":"Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, et al. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013;10:813\u20134.","journal-title":"Nat Methods"},{"key":"613_CR14","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1093\/bioinformatics\/btt004","volume":"29","author":"N Thomas","year":"2013","unstructured":"Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: A tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics. 2013;29:542\u201350.","journal-title":"Bioinformatics"},{"issue":"D","key":"613_CR15","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1186\/1471-2164-15-409","volume":"15","author":"M Giraud","year":"2014","unstructured":"Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A, et al. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics. 2014;15(D):409.","journal-title":"BMC Genomics"},{"issue":"May","key":"613_CR16","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1093\/nar\/gkt382","volume":"41","author":"J Ye","year":"2013","unstructured":"Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013;41(May):34\u201340.","journal-title":"Nucleic Acids Res"},{"key":"613_CR17","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btq056","volume":"26","author":"S Munshaw","year":"2010","unstructured":"Munshaw S, Kepler TB. SoDA2: A Hidden Markov Model approach for identification of immunoglobulin rearrangements. Bioinformatics. 2010;26:867\u201372.","journal-title":"Bioinformatics"},{"key":"613_CR18","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1093\/bioinformatics\/btm147","volume":"23","author":"BA Ga\u00ebta","year":"2007","unstructured":"Ga\u00ebta BA, Malming HR, Jackson KJL, Bain ME, Wilson P, Collins AM. iHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics. 2007;23:1580\u20137.","journal-title":"Bioinformatics"},{"key":"613_CR19","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1186\/1471-2164-12-106","volume":"12","author":"P Nguyen","year":"2011","unstructured":"Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics. 2011;12:106.","journal-title":"BMC Genomics"},{"key":"613_CR20","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nmeth.2960","volume":"11","author":"M Shugay","year":"2014","unstructured":"Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, Mamedov IZ, Tuganbaev TR, et al. Towards error-free profiling of immune repertoires. Nat Methods. 2014;11:653\u20135.","journal-title":"Nat Methods"},{"key":"613_CR21","doi-asserted-by":"crossref","unstructured":"Calis JJA., Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol. 2014;35:581\u201390.","DOI":"10.1016\/j.it.2014.09.004"},{"key":"613_CR22","doi-asserted-by":"publisher","first-page":"5980","DOI":"10.1073\/pnas.1319389111","volume":"111","author":"IV Zvyagin","year":"2014","unstructured":"Zvyagin IV, Pogorelyy MV, Ivanova ME, Komech E, Shugay M, Bolotin DA, et al. Distinctive properties of identical twins\u2019 TCR repertoires revealed by high-throughput sequencing. Proc Natl Acad Sci U S A. 2014;111:5980\u20135.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"December","key":"613_CR23","first-page":"463","volume":"4","author":"EV Putintseva","year":"2013","unstructured":"Putintseva EV, Britanova OV, Staroverov DB, Merzlyak EM, Turchaninova MA, Shugay M, et al. Mother and child T cell receptor repertoires: deep profiling study. Front Immunol. 2013;4(December):463.","journal-title":"Front Immunol"},{"key":"613_CR24","unstructured":"R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2014. http:\/\/www.R-project.org\/"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0613-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0613-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0613-1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0613-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T07:55:59Z","timestamp":1566892559000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0613-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,28]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["613"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0613-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,5,28]]},"assertion":[{"value":"20 March 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 May 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"175"}}