Tools and Resources
Various tools and resources that the group has developed or contributed to:
- OGRDB:
the
Open Germline Receptor Database. Developed
by group member Dr William Lees with input from members of the AIRR
Community and hosted at Birkbeck.
Lees, W., Busse, C. E., Corcoran, M., Ohlin, M., Scheepers, C., Matsen IV, F. A., Yaari, G., Watson, C. T., The AIRR Community, Collins, A., Shepherd, A. J. (2019). OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Research gkz822. - VDJbase: the
adaptive immune receptor Genotype and Haplotype database. Originally
developed by Gur Yaari's lab, now jointly maintained and developed by group member Dr
William Lees, and hosted at Birkbeck.
Omer, A., Shemesh, O., Peres, A., Polak, P., Shepherd, A. J., Watson, C. T., Boyd, S. D., Collins, A. M., Lees, W. and Yaari, G. (2019). VDJbase: an adaptive immune receptor (AIR) genotype and haplotype database. Nucleic Acids Research gkz872. - sumrep: a
summary statistic framework for BCR and TCR repertoires. Developed
by the Matsen Group with input from us and from other members of the
AIRR Community.
Olson, B. J., Moghimi, P., Schramm, C., Obraztsova, A., Ralph, D., Vander Heiden, J. A., Shugay, M., Shepherd, A., Lees, W., Matsen IV, F. A. (2019). sumrep: a summary statistic framework for immune receptor repertoire comparison and model validation. Frontiers in Immunology 10:02533. - TRIgS:
tools for the
high throughput analysis of antibody repertoires.
Lees, W.D., Shepherd, A.J. (2015). Utilities for high-throughput analysis of B-cell clonal lineages. Journal of Immunology Research, Article ID 323506
