Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes
Calculate SNPs or their count for each germline-input sequence pair wi...
Calculate SNPs or their count for each germline-input sequence pair wi...
Calculate differences between characters in columns of germs and retur...
Calculate differences between characters in columns of germs and retur...
Alleles nucleotide position difference
Allele similarity cluster naming scheme
FWR1 artificial dataset generator
Assign allele similarity clusters
Extracts the allele cluster table from the archive file.
Generate allele similarity reference set
Converts IGHV germline set to ASC germline set.
Output of inferAlleleClusters
Allele similarity clustering
Germline set alleles distance
Allele similarity cluster
Allele similarity cluster based genotype inference Testing function
Allele based genotype inference
Insert gaps into an ungapped sequence based on a gapped reference sequ...
piglet: Program for Inferring Immunoglobulin Allele Similarity Cluster...
The Program for Ig clusters (PIgLET) package
Pipe operator
Plotting the dendrogram of the clusters
Retrieving allele similarity clusters Zenodo archive
zenodoArchive
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>.