The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
Open accessAbstract
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.
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A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486
SIMPSON, E. H. (1949) · Nature · doi:10.1038/163688a0 · Cited by 14,164
Gotelli, N. J., & Colwell, R. K. (2001) · Ecology Letters · doi:10.1046/j.1461-0248.2001.00230.x · Cited by 6,420
THE DISTRIBUTION OF THE FLORA IN THE ALPINE ZONE. 1
Jaccard, P. (1912) · New Phytologist · doi:10.1111/j.1469-8137.1912.tb05611.x · Cited by 4,561
Colwell, R. K., Chao, A., Gotelli, N. J., Lin, S.-Y., Mao, C. X., Chazdon, R. L., & Longino, J. T. (2012) · Journal of Plant Ecology · doi:10.1093/jpe/rtr044 · Cited by 1,921
MiXCR: software for comprehensive adaptive immunity profiling
Bolotin, D. A., Poslavsky, S., Mitrophanov, I., Shugay, M., Mamedov, I. Z., Putintseva, E. V., & Chudakov, D. M. (2015) · Nature Methods · doi:10.1038/nmeth.3364 · Cited by 1,722
Self-citationMeasurement of "Overlap" in Comparative Ecological Studies
Horn, H. S. (1966) · The American Naturalist · doi:10.1086/282436 · Cited by 1,613
Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity
Hughes, J. B., Hellmann, J. J., Ricketts, T. H., & Bohannan, B. J. M. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.10.4399-4406.2001 · Cited by 1,296
IgBLAST: an immunoglobulin variable domain sequence analysis tool
Ye, J., Ma, N., Madden, T. L., & Ostell, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt382 · Cited by 1,189
Detection and quantification of rare mutations with massively parallel sequencing
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105422108 · Cited by 1,144
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Self-citationTwo subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans
Galletti, G., De Simone, G., Mazza, E. M. C., Puccio, S., Mezzanotte, C., Bi, T. M., Davydov, A. N., Metsger, M., Scamardella, E., Alvisi, G., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0791-5 · Cited by 299
Self-citationOverview of methodologies for T-cell receptor repertoire analysis
Rosati, E., Dowds, C. M., Liaskou, E., Henriksen, E. K. K., Karlsen, T. H., & Franke, A. (2017) · BMC Biotechnology · doi:10.1186/s12896-017-0379-9 · Cited by 322
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Patil, V. S., Madrigal, A., Schmiedel, B. J., Clarke, J., O’Rourke, P., de Silva, A. D., Harris, E., Peters, B., Seumois, G., Weiskopf, D., et al. (2018) · Science Immunology · doi:10.1126/sciimmunol.aan8664 · Cited by 262
Metadata
- Authors
- Shugay, M., Bagaev, D. V., Turchaninova, M. A., Bolotin, D. A., Britanova, O. V., Putintseva, E. V., Pogorelyy, M. V., Nazarov, V. I., Zvyagin, I. V., Kirgizova, V. I., Kirgizov, K. I., Skorobogatova, E. V., & Chudakov, D. M.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-11-25
- Volume
- 11
- Issue
- 11
- Pages
- e1004503
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2185265351
- Cited by
- 614
- References
- 60
- FWCI
- 11.13
- Type
- journal article
- Language
- en
- Open access
- gold
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- Shugay, M., Bagaev, D. V., Turchaninova, M. A., Bolotin, D. A., Britanova, O. V., Putintseva, E. V., Pogorelyy, M. V., Nazarov, V. I., Zvyagin, I. V., Kirgizova, V. I., Kirgizov, K. I., Skorobogatova, E. V., & Chudakov, D. M. (2015). VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1004503
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