R-universe - ayeletperes (Ayelet Peres)

piglet - Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires. The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes. The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.

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5.72 score 50 scripts 314 downloads

rabhit - Inference Tool for Antibody Haplotype

Infers V-D-J haplotypes and gene deletions from AIRR-seq data for Ig and TR chains, based on J, D, or V genes as anchor, by adapting a Bayesian framework. It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene. Citation: Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>. Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.

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4.20 score 16 scripts 292 downloads