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README.md
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@@ -20,9 +20,10 @@ Benchmark datasets from various AIRR tools and algorithms, including, but not li
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* GLIPH/GLIPH2
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* pyigmap
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Note on some
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* ``gliph/`` data comes from [Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, Ji X, Han A, Krams SM, Pettus C, Haas N, Arlehamn CSL, Sette A, Boyd SD, Scriba TJ, Martinez OM, Davis MM. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017 Jul 6;547(7661):94-98. doi:10.1038/nature22976](https://doi.org/10.1038/nature22976) and [Huang H, Wang C, Rubelt F, Scriba TJ, Davis MM. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat Biotechnol. 2020 Oct;38(10):1194-1202. doi: 10.1038/s41587-020-0505-4.](https://doi.org/10.1038/s41587-020-0505-4)
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* ``alice/mlr`` data comes from [Emerson RO, Mathew JM, Konieczna IM, Robins HS, Leventhal JR. Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture. PLoS One. 2014 Nov 3;9(11):e111943. doi: 10.1371/journal.pone.0111943
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* ``dcode/`` data from [10X Genomics](https://www.10xgenomics.com/datasets/cd-8-plus-t-cells-of-healthy-donor-1-1-standard-3-0-2)
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* ``vdjtools/SRR*`` data from [Qi Q, Liu Y, Cheng Y, Glanville J, Zhang D, Lee JY, Olshen RA, Weyand CM, Boyd SD, Goronzy JJ. Diversity and clonal selection in the human T-cell repertoire. Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13139-44. doi: 10.1073/pnas.1409155111
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* ``vdjtools/A*`` data from [Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J Immunol. 2016 Jun 15;196(12):5005-13. doi: 10.4049/jimmunol.1600005](https://doi.org/10.4049/jimmunol.1600005)
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* GLIPH/GLIPH2
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* pyigmap
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Note on some datasets used:
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* ``gliph/`` data comes from [Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, Ji X, Han A, Krams SM, Pettus C, Haas N, Arlehamn CSL, Sette A, Boyd SD, Scriba TJ, Martinez OM, Davis MM. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017 Jul 6;547(7661):94-98. doi:10.1038/nature22976](https://doi.org/10.1038/nature22976) and [Huang H, Wang C, Rubelt F, Scriba TJ, Davis MM. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat Biotechnol. 2020 Oct;38(10):1194-1202. doi: 10.1038/s41587-020-0505-4.](https://doi.org/10.1038/s41587-020-0505-4)
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* ``alice/mlr`` data comes from [Emerson RO, Mathew JM, Konieczna IM, Robins HS, Leventhal JR. Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture. PLoS One. 2014 Nov 3;9(11):e111943. doi: 10.1371/journal.pone.0111943](https://dx.plos.org/10.1371/journal.pone.0111943)
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* ``dcode/`` data from [10X Genomics](https://www.10xgenomics.com/datasets/cd-8-plus-t-cells-of-healthy-donor-1-1-standard-3-0-2)
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* ``vdjtools/SRR*`` data from [Qi Q, Liu Y, Cheng Y, Glanville J, Zhang D, Lee JY, Olshen RA, Weyand CM, Boyd SD, Goronzy JJ. Diversity and clonal selection in the human T-cell repertoire. Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13139-44. doi: 10.1073/pnas.1409155111](https://doi.org/10.1073/pnas.1409155111)
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* ``vdjtools/A*`` data from [Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J Immunol. 2016 Jun 15;196(12):5005-13. doi: 10.4049/jimmunol.1600005](https://doi.org/10.4049/jimmunol.1600005)
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* ``tcrnet/`` data from [Emerson RO, DeWitt WS, Vignali M, Gravley J, Hu JK, Osborne EJ, Desmarais C, Klinger M, Carlson CS, Hansen JA, Rieder M, Robins HS. Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet. 2017 May;49(5):659-665. doi: 10.1038/ng.3822](https://doi.org/10.1038/ng.3822)
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