Package: piglet 1.3.0

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>.

Authors:Ayelet Peres [aut, cre], William Lees [aut], Gur Yaari [aut, cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
piglet/json (API)

# Install 'piglet' in R:
install.packages('piglet', repos = c('https://ayeletperes.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ayeletperes/piglet/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

5.25 score 44 scripts 268 downloads 32 exports 103 dependencies

Last updated from:45063019e3. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK343
linux-devel-x86_64OK375
source / vignettesOK378
linux-release-arm64OK353
linux-release-x86_64OK425
macos-release-arm64OK230
macos-release-x86_64OK417
macos-oldrel-arm64OK213
macos-oldrel-x86_64OK368
windows-develOK355
windows-releaseOK335
windows-oldrelOK332
wasm-releaseOK223

Exports:%>%allele_diffallele_diff_indicesallele_diff_indices_parallelallele_diff_indices_parallel2allele_diff_stringsalleleClusterNamesallelePaletteartificialFRW1GermlineassignAlleleClustersdetect_communities_leidendistance_to_graphextractASCTablegenotypeToTiggergermlineASCigClustigDistanceighvClustighvDistanceinferAlleleClustersinferGenotypeAlleleinferGenotypeAllele_ascinsert_gaps2_vecnew_germline_clusteroptimize_resolutionplotClusterComparisonplotCommunityNetworkplotGenotypeAlleleplotSilhouetteOptimizationplotTruncatedTreerecentAlleleClusterszenodoArchive

Dependencies:abindade4airralakazamapeBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopscigarillocirclizeclicliprclustercodetoolscolorspacecpp11crayondata.tableDBIDECIPHERDelayedArraydendextenddigestdoParalleldplyrfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2GlobalOptionsgluegridExtragtablegtoolshmsigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsnlmepillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsS7scalessegmentedSeqinfoseqinrshapesnowspSparseArraystringdiststringistringrSummarizedExperimenttibbletidyrtidyselecttiggertzdbutf8vctrsviridisviridisLitevroomwithrXVectoryaml

Generating Allele Similarity Clusters (ASC) for BIOMED IGHV Reference
Overview
Rendered fromPIgLET_biomed_asc.Rmdusingknitr::rmarkdown

Last update: 2026-02-23
Started: 2025-07-08

PIgLET: Program for Ig clusters
Introduction | Package Overview | Allele Similarity Cluster: | Allele based genotype: | Allele Similarity Cluster | Library amplicon length | Inferring Allele Similarity Clusters | Artificial framework 1 reference set | Allele based genotype | ASC-based thresholds | Introduction | Retriving Zenodo archive | Inferring ASC-based genotype | Contact | References
Rendered fromPIgLET-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-02-23
Started: 2023-06-09

Readme and manuals

Help Manual

Help pageTopics
Allele similarity cluster tableallele_cluster_table
Alleles nucleotide position differenceallele_diff
Calculate differences between characters in columns of germs and return their indices as an int vector.allele_diff_indices
Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.allele_diff_indices_parallel
Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.allele_diff_indices_parallel2
Calculate differences between characters in columns of germs and return them as a string vector.allele_diff_strings
Allele thresholds tableallele_threshold_table
Allele similarity cluster naming schemealleleClusterNames
Allele color paletteallelePalette
FWR1 artificial dataset generatorartificialFRW1Germline
Assign allele similarity clustersassignAlleleClusters
Leiden community detectiondetect_communities_leiden
Convert distance matrix to weighted graphdistance_to_graph
Extracts the allele cluster table from the archive file.extractASCTable
Generate allele similarity reference setgenerateReferenceSet
Convert a PIgLET genotype to a TIgGER/VDJbase genotype tablegenotypeToTigger
Converts IGHV germline set to ASC germline set.germlineASC
Human IGHV germlines functionality descriptionhv_functionality
Human IGHV germlinesHVGERM
Allele similarity clusteringigClust
Germline set alleles distanceigDistance
Allele similarity clustering (deprecated)ighvClust
Germline set alleles distance (deprecated)ighvDistance
Allele similarity clusterinferAlleleClusters
Allele based genotype inferenceinferGenotypeAllele
Allele similarity cluster based genotype inference Testing functioninferGenotypeAllele_asc
Insert gaps into an ungapped sequence based on a gapped reference sequence.insert_gaps2_vec
Create a GermlineCluster objectnew_germline_cluster
Optimize resolution parameter using silhouette scoreoptimize_resolution
The Program for Ig clusters (PIgLET) packagepiglet
Plot method for GermlineClusterplot.GermlineCluster
Plotting the dendrogram of the clustersplotAlleleCluster
Compare hierarchical and Leiden clusteringplotClusterComparison
Plot community networkplotCommunityNetwork
Plot a PIgLET genotype with a per-allele confidence panelplotGenotypeAllele
Plot silhouette optimization resultsplotSilhouetteOptimization
Plot truncated tree visualizationplotTruncatedTree
Print method for GermlineClusterprint.GermlineCluster
Retrieving allele similarity clusters Zenodo archiverecentAlleleClusters
Summary method for GermlineClustersummary.GermlineCluster
zenodoArchivezenodoArchive