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PIgLET - Program for Ig clusters R package

PIgLET is a suite of computational tools that improves genotype inference and downstream AIRR-seq data analysis. The package as two main tools. The first is Allele Clusters, this tool is designed to reduce the ambiguity within the IGHV 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.

Core Abilities

Allele Similarity Cluster provides the functions that support the main tool of creating the allele similarity cluster form an IGHV germline set. Allele based genotype provides the functions to infer the IGHV genotype using the allele based method and the allele clusters thresholds.

Required Input

For the allele similarity cluster, a reference set of IUIS/IMGT alleles. The sequences should be gapped.

For the genotype inference, an AIRR-seq format data set.

Installation

PIgLET is available for installation either from the development version.

PIgLET repository installation

To build from the source code, first install the build dependencies:

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown", "plotly"))

To install the latest version via devtools:

library(devtools)
install_bitbucket("yaarilab/piglet")

Note, installing from bitbucket does not generate the documentation. To generate them, first clone the repository and then build:

library(devtools)
install_deps()
document()
build()
install()

Contact

For help, questions, or suggestions, please contact:

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Version

Install

install.packages('piglet')

Monthly Downloads

39

Version

1.2.0

License

CC BY-SA 4.0

Maintainer

Ayelet Peres

Last Published

February 17th, 2026

Functions in piglet (1.2.0)

inferGenotypeAllele_asc

Allele similarity cluster based genotype inference Testing function

hv_functionality

Human IGHV germlines functionality description

Germline set alleles distance

Allele similarity clustering (deprecated)

Allele similarity clustering

inferGenotypeAllele

Allele based genotype inference

inferAlleleClusters

Allele similarity cluster

optimize_resolution

Optimize resolution parameter using silhouette score

plotTruncatedTree

Plot truncated tree visualization

plotCommunityNetwork

Plot community network

plot.GermlineCluster

Plot method for GermlineCluster

plotClusterComparison

Compare hierarchical and Leiden clustering

plotSilhouetteOptimization

Plot silhouette optimization results

The Program for Ig clusters (PIgLET) package

plotAlleleCluster

Plotting the dendrogram of the clusters

piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

summary.GermlineCluster

Summary method for GermlineCluster

print.GermlineCluster

Print method for GermlineCluster

recentAlleleClusters

Retrieving allele similarity clusters Zenodo archive

allele_diff_indices_parallel2

Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.

allele_diff_strings

Calculate differences between characters in columns of germs and return them as a string vector.

allele_diff_indices_parallel

Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.

Alleles nucleotide position difference

GermlineCluster

GermlineCluster class

alleleClusterNames

Allele similarity cluster naming scheme

allele_diff_indices

Calculate differences between characters in columns of germs and return their indices as an int vector.

extractASCTable

Extracts the allele cluster table from the archive file.

artificialFRW1Germline

FWR1 artificial dataset generator

assignAlleleClusters

Assign allele similarity clusters

new_germline_cluster

Create a GermlineCluster object

insert_gaps2_vec

Insert gaps into an ungapped sequence based on a gapped reference sequence.

distance_to_graph

Convert distance matrix to weighted graph

compute_distance

Compute distance matrix

Find resolution for target cluster count

Human IGHV germlines

.create_iuis_labels_with_markers

Create IUIS labels with markers for split groups

allele_threshold_table

Allele thresholds table

allele_cluster_table

Allele similarity cluster table

generateReferenceSet

Generate allele similarity reference set

Converts IGHV germline set to ASC germline set.

Germline set alleles distance (deprecated)

detect_communities_leiden

Leiden community detection