{ "_id": "6ac89cf8de46216d5edd48df", "Package": "piglet", "Title": "Program for Inferring Immunoglobulin Allele Similarity Clusters\nand Genotypes", "Version": "1.5.2", "Authors@R": "c(person(\"Ayelet\", \"Peres\", role=c(\"aut\",\"cre\"),\nemail=\"ayelet.peres@yale.edu\"),\nperson(\"William\", \"Lees\", role=c(\"aut\"),\nemail=\"william@lees.org.uk\"),\nperson(\"Gur\", \"Yaari\", role=c(\"aut\",\"cph\"),\nemail=\"gur.yaari@yale.edu\"))", "Author": "Ayelet Peres [aut, cre], William Lees [aut], Gur Yaari [aut,\ncph]", "Maintainer": "Ayelet Peres ", "Description": "Improves genotype inference and downstream Adaptive Immune\nReceptor Repertoire Sequence data analysis. Inference of allele\nsimilarity clusters, an alternative naming scheme and genotype\ninference for immunoglobulin heavy chain repertoires. The main\ntools are allele similarity clusters, and allele based\ngenotype. The first tool is designed to reduce the ambiguity\nwithin the immunoglobulin heavy chain V alleles. The ambiguity\nis caused by duplicated or similar alleles which are shared\namong different genes. The second tool is an allele based\ngenotype, that determined the presence of an allele based on a\nthreshold derived from a naive population. See Peres et al.\n(2023) .", "License": "CC BY-SA 4.0", "URL": "https://github.com/ayeletperes/piglet", "BugReports": "https://github.com/ayeletperes/piglet/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "GNU make", "RoxygenNote": "7.3.3", "Collate": "'Data.R' 'GermlineCluster-class.R' 'RcppExports.R' 'piglet.R'\n'allele_cluster.R' 'utils.R' 'allele_genotype.R'\n'asc_iuis_labels.R' 'asc_regroup.R' 'community_detection.R'\n'deprecated.R' 'piglet-package.R' 'qtl_pairing.R'\n'qtl_pairing_leads.R' 'qtl_scan.R' 'qtl_usage.R' 'utils-pipe.R'\n'visualization.R'", "LazyData": "true", "BuildVignettes": "true", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libglpk-dev make libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://ayeletperes.r-universe.dev", "Date/Publication": "2026-09-27 22:22:20 UTC", "RemoteUrl": "https://github.com/ayeletperes/piglet", "RemoteRef": "HEAD", "RemoteSha": "39d6600e67d99159f4185d830607c96be163d191", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-08 11:59:47 UTC", "User": "root" }, "_user": "ayeletperes", "_type": "src", "_file": "piglet_1.5.2.tar.gz", "_fileid": "https://r2.ropensci.org/5fc80a1131bb63542713ffcf34aa032af03ed9c3df27db8badbcb47f32ce51e0", "_filesize": 2775654, "_sha256": "5fc80a1131bb63542713ffcf34aa032af03ed9c3df27db8badbcb47f32ce51e0", "_expires": "2027-01-16T12:14:49.000Z", "_created": "2026-10-08T11:59:47.000Z", "_published": "2026-10-09T07:51:20.515Z", "_buildurl": "https://github.com/r-universe/ayeletperes/actions/runs/37773195106", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113721834707, "time": 253, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11548862031" }, { "job": 113721833784, "time": 326, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11549990830" }, { "job": 113721834791, "time": 275, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11549526144" }, { "job": 113721834583, "time": 307, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11549940771" }, { "job": 113721835060, "time": 278, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11549002937" }, { "job": 113721833932, "time": 713, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11549667380" }, { "job": 113721834665, "time": 309, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11549481670" }, { "job": 113721832603, "time": 383, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11602342032" }, { "job": 113721833942, "time": 332, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11548826343" }, { "job": 113721834755, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11549475709" }, { "job": 113721833890, "time": 483, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11549386728" }, { "job": 113721834094, "time": 317, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11549246888" }, { "job": 113721834295, "time": 265, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11549206742" }, { "job": 113721834444, "time": 503, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11549531664" }, { "job": 113721833933, "time": 297, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11549526206" } ], "_upstream": "https://github.com/ayeletperes/piglet", "_commit": { "id": "39d6600e67d99159f4185d830607c96be163d191", "author": "ayelet peres ", "committer": "ayelet peres ", "message": "fix: stop inferGenotypeAllele() duplicating rows and inflating depth\n\nTwo bugs in the threshold-table handling, both found by asking whether the merge\nat the end of the genotype path could change row counts.\n\n1. Duplicated rows and wrong depth. The threshold table is joined into the\n genotype counts with all.x = TRUE, so a repeated join key produced one output\n row per threshold row, each carrying that allele's whole count. The duplicate\n rows were identical in all eight output columns, carrying no information.\n\n The damage was not the duplicates. Depth is a per-locus denominator shared by\n every row, so all rows reported it inflated and z_score moved with it, which\n means the genotype call could change. Measured on 22 + 20 reads:\n\n alleles sharing a cluster depth reported cluster z_score\n 1 42 (true) 339.4\n 2 64 274.9\n 3 86 237.2\n 4 108 211.6\n\n Two triggers. With asc_annotation = TRUE the key is asc_allele, which is\n non-unique by design, and the bundled table has seven such rows. With\n asc_annotation = FALSE the key is allele, which a caller's table can repeat;\n all four threshold tables in this project happen to be unique there, which is\n why the default path looked fine.\n\n Fixed by reducing to one row per genotyped allele before the join. Verified\n byte-identical to 1.5.1 output where the key was already unique, so this only\n moves the cases that were wrong.\n\n2. Hard error on a table without asc_allele. When an allele in the data was not\n in the threshold table, the appended row named asc_allele literally, so a\n three-column table received a four-column row and rbind failed with a\n column-count message from inside rbindlist. The row is now built from the\n table's own columns.\n\n Worth recording that the same question", "time": 1790547740 }, "_maintainer": { "name": "Ayelet Peres", "email": "ayelet.peres@yale.edu", "login": "ayeletperes", "description": "Computational biologist @ Yale. Yaari & Kleinstein labs. AIRR-seq tools: Ig germline references, allele inference, genotyping, haplotypes.", "uuid": 26592225 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Biostrings", "version": ">= 2.62.0", "role": "Imports" }, { "package": "DECIPHER", "version": ">= 2.22.0", "role": "Imports" }, { "package": "alakazam", "version": ">= 1.2.0", "role": "Imports" }, { "package": "dendextend", "version": ">= 1.9.0", "role": "Imports" }, { "package": "data.table", "version": ">= 1.12.2", "role": "Imports" }, { "package": "tigger", "version": ">= 1.0.0", "role": "Imports" }, { "package": "methods", "version": ">= 3.4.4", "role": "Imports" }, { "package": "rlang", "version": ">= 0.4.0", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1.2", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.3.6", "role": "Imports" }, { "package": "circlize", "version": ">= 0.4.15", "role": "Imports" }, { "package": "gridExtra", "version": ">= 2.3", "role": "Imports" }, { "package": "R6", "version": ">= 2.5.1", "role": "Imports" }, { "package": "jsonlite", "version": ">= 1.8.3", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.11.0", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "igraph", "version": ">= 1.3.0", "role": "Imports" }, { "package": "stringdist", "version": ">= 0.9.0", "role": "Imports" }, { "package": "cluster", "version": ">= 2.1.0", "role": "Imports" }, { "package": "ape", "version": ">= 5.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "ggtree", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ayeletperes", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-07", "n": 2 }, { "week": "2026-09", "n": 3 }, { "week": "2026-25", "n": 12 }, { "week": "2026-29", "n": 1 }, { "week": "2026-33", "n": 1 }, { "week": "2026-38", "n": 2 }, { "week": "2026-39", "n": 4 } ], "_tags": [ { "name": "v1.5.0", "date": "2026-09-14" }, { "name": "v1.5.1", "date": "2026-09-25" }, { "name": "v1.5.2", "date": "2026-09-27" } ], "_stars": 0, "_contributors": [ { "user": "ayeletperes", "count": 91, "uuid": 26592225 } ], "_userbio": { "uuid": 26592225, "type": "user", "name": "Ayelet Peres", "followers": 1, "description": "Computational biologist @ Yale. 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"allele_diff_strings", "alleleClusterNames", "allelePalette", "annotateRepertoireIUIS", "artificialFRW1Germline", "ascIUISVocabulary", "ascUsagePhenotype", "assignAlleleClusters", "detect_communities_leiden", "distance_to_graph", "extractASCTable", "genotypeToTigger", "germlineASC", "igClust", "igDistance", "ighvClust", "ighvDistance", "inferAlleleClusters", "inferGenotypeAllele", "inferGenotypeAllele_asc", "insert_gaps", "insert_gaps2_vec", "new_germline_cluster", "optimize_resolution", "pairingCellTests", "pairingLeadCharacter", "pairingPhenotype", "pairingScan", "pairingTable", "plotClusterComparison", "plotCommunityNetwork", "plotGenotypeAllele", "plotSilhouetteOptimization", "plotTruncatedTree", "qtlClump", "qtlLDGroups", "qtlScanMultivariate", "qtlScanUnivariate", "qtlSmallestGenotypeClass", "recentAlleleClusters", "regroupASCByLabel", "runGeneUsageQTL", "runPairingQTL", "zenodoArchive" ], "_datasets": [ { "name": "allele_cluster_table", "title": "Allele similarity cluster table", "object": "allele_cluster_table", "class": [ "data.table", "data.frame" ], "fields": [ "new_allele", "func_group", "imgt_allele", "thresh", "amplicon_length" ], "rows": 286, "table": true, "tojson": true }, { "name": "allele_threshold_table", "title": "Allele thresholds table", "object": "allele_threshold_table", "class": [ "data.table", "data.frame" ], "fields": [ "allele", "asc_allele", "threshold", "tag" ], "rows": 262, "table": true, "tojson": true }, { "name": "hv_functionality", "title": "Human IGHV germlines functionality description", "object": "hv_functionality", "class": [ "data.table", "data.frame" ], "fields": [ "allele", "functional", "nt_sequence", "aa_sequence" ], "rows": 521, "table": true, "tojson": true }, { "name": "HVGERM", "title": "Human IGHV germlines", "object": "HVGERM", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "allele_cluster_table", "title": "Allele similarity cluster table", "topics": [ "allele_cluster_table" ] }, { "page": "allele_diff", "title": "Alleles nucleotide position difference", "topics": [ "allele_diff" ] }, { "page": "allele_diff_indices", "title": "Calculate differences between characters in columns of germs and return their indices as an int vector.", "topics": [ "allele_diff_indices" ] }, { "page": "allele_diff_indices_parallel", "title": "Deprecated: use 'allele_diff_paired'", "topics": [ "allele_diff_indices_parallel" ] }, { "page": "allele_diff_indices_parallel2", "title": "Deprecated: use 'allele_diff_paired'", "topics": [ "allele_diff_indices_parallel2" ] }, { "page": "allele_diff_paired", "title": "Count or locate SNPs between paired germline and input sequences", "topics": [ "allele_diff_paired" ] }, { "page": "allele_diff_strings", "title": "Calculate differences between characters in columns of germs and return them as a string vector.", "topics": [ "allele_diff_strings" ] }, { "page": "allele_threshold_table", "title": "Allele thresholds table", "topics": [ "allele_threshold_table" ] }, { "page": "alleleClusterNames", "title": "Allele similarity cluster naming scheme", "topics": [ "alleleClusterNames" ] }, { "page": "allelePalette", "title": "Allele color palette", "topics": [ "allelePalette" ] }, { "page": "annotateRepertoireIUIS", "title": "Add IUIS gene-group columns to a genotype-corrected repertoire", "topics": [ "annotateRepertoireIUIS" ] }, { "page": "artificialFRW1Germline", "title": "FWR1 artificial dataset generator", "topics": [ "artificialFRW1Germline" ] }, { "page": "ascIUISVocabulary", "title": "Build the ASC subgroup to IUIS gene-group vocabulary", "topics": [ "ascIUISVocabulary" ] }, { "page": "ascUsagePhenotype", "title": "Per-subject usage of each gene group", "topics": [ "ascUsagePhenotype" ] }, { "page": "assignAlleleClusters", "title": "Assign allele similarity clusters", "topics": [ "assignAlleleClusters" ] }, { "page": "detect_communities_leiden", "title": "Leiden community detection", "topics": [ "detect_communities_leiden" ] }, { "page": "distance_to_graph", "title": "Convert distance matrix to weighted graph", "topics": [ "distance_to_graph" ] }, { "page": "extractASCTable", "title": "Extracts the allele cluster table from the archive file.", "topics": [ "extractASCTable" ] }, { "page": "generateReferenceSet", "title": "Generate allele similarity reference set", "topics": [ "generateReferenceSet" ] }, { "page": "genotypeToTigger", "title": "Convert a PIgLET genotype to a TIgGER/VDJbase genotype table", "topics": [ "genotypeToTigger" ] }, { "page": "germlineASC", "title": "Converts IGHV germline set to ASC germline set.", "topics": [ "germlineASC" ] }, { "page": "hv_functionality", "title": "Human IGHV germlines functionality description", "topics": [ "hv_functionality" ] }, { "page": "HVGERM", "title": "Human IGHV germlines", "topics": [ "HVGERM" ] }, { "page": "igClust", "title": "Allele similarity clustering", "topics": [ "igClust" ] }, { "page": "igDistance", "title": "Germline set alleles distance", "topics": [ "igDistance" ] }, { "page": "ighvClust", "title": "Allele similarity clustering (deprecated)", "topics": [ "ighvClust" ] }, { "page": "ighvDistance", "title": "Germline set alleles distance (deprecated)", "topics": [ "ighvDistance" ] }, { "page": "inferAlleleClusters", "title": "Allele similarity cluster", "topics": [ "inferAlleleClusters" ] }, { "page": "inferGenotypeAllele", "title": "Allele based genotype inference", "topics": [ "inferGenotypeAllele" ] }, { "page": "inferGenotypeAllele_asc", "title": "Allele similarity cluster based genotype inference Testing function", "topics": [ "inferGenotypeAllele_asc" ] }, { "page": "insert_gaps", "title": "Insert gaps into an ungapped sequence based on a gapped reference sequence.", "topics": [ "insert_gaps" ] }, { "page": "insert_gaps2_vec", "title": "Deprecated: use 'insert_gaps'", "topics": [ "insert_gaps2_vec" ] }, { "page": "new_germline_cluster", "title": "Create a GermlineCluster object", "concept": [ "GermlineCluster" ], "topics": [ "new_germline_cluster" ] }, { "page": "optimize_resolution", "title": "Optimize resolution parameter using silhouette score", "topics": [ "optimize_resolution" ] }, { "page": "pairingCellTests", "title": "Per-cell follow-up under a significant pairing hit", "topics": [ "pairingCellTests" ] }, { "page": "pairingLeadCharacter", "title": "Characterise pairing leads: what kind of signal is this?", "topics": [ "pairingLeadCharacter" ] }, { "page": "pairingPhenotype", "title": "The response matrix for one anchor gene", "topics": [ "pairingPhenotype" ] }, { "page": "pairingScan", "title": "Scan variants against a gene's partner distribution", "topics": [ "pairingScan" ] }, { "page": "pairingTable", "title": "Observed against expected gene pairing, per subject", "topics": [ "pairingTable" ] }, { "page": "piglet", "title": "The Program for Ig clusters (PIgLET) package", "topics": [ "piglet" ] }, { "page": "plot.GermlineCluster", "title": "Plot method for GermlineCluster", "topics": [ "plot.GermlineCluster" ] }, { "page": "plotAlleleCluster", "title": "Plotting the dendrogram of the clusters", "topics": [ "plotAlleleCluster" ] }, { "page": "plotClusterComparison", "title": "Compare hierarchical and Leiden clustering", "topics": [ "plotClusterComparison" ] }, { "page": "plotCommunityNetwork", "title": "Plot community network", "topics": [ "plotCommunityNetwork" ] }, { "page": "plotGenotypeAllele", "title": "Plot a PIgLET genotype with a per-allele confidence panel", "topics": [ "plotGenotypeAllele" ] }, { "page": "plotSilhouetteOptimization", "title": "Plot silhouette optimization results", "topics": [ "plotSilhouetteOptimization" ] }, { "page": "plotTruncatedTree", "title": "Plot truncated tree visualization", "topics": [ "plotTruncatedTree" ] }, { "page": "print.GermlineCluster", "title": "Print method for GermlineCluster", "topics": [ "print.GermlineCluster" ] }, { "page": "qtlClump", "title": "Independent lead variants by greedy clumping", "topics": [ "qtlClump" ] }, { "page": "qtlLDGroups", "title": "Collapse variants carrying identical genotype information", "topics": [ "qtlLDGroups" ] }, { "page": "qtlScanMultivariate", "title": "Multivariate QTL scan by Pillai's trace", "topics": [ "qtlScanMultivariate" ] }, { "page": "qtlScanUnivariate", "title": "Univariate QTL scan of every phenotype on every variant", "topics": [ "qtlScanUnivariate" ] }, { "page": "qtlSmallestGenotypeClass", "title": "Smallest observed genotype class per variant", "topics": [ "qtlSmallestGenotypeClass" ] }, { "page": "recentAlleleClusters", "title": "Retrieving allele similarity clusters Zenodo archive", "topics": [ "recentAlleleClusters" ] }, { "page": "regroupASCByLabel", "title": "Regroup Allele Similarity Clusters by a per-allele label", "topics": [ "regroupASCByLabel" ] }, { "page": "runGeneUsageQTL", "title": "Gene-usage QTL scan for one locus", "topics": [ "runGeneUsageQTL" ] }, { "page": "runPairingQTL", "title": "Conditional gene-pairing QTL scan for one anchoring", "topics": [ "runPairingQTL" ] }, { "page": "summary.GermlineCluster", "title": "Summary method for GermlineCluster", "topics": [ "summary.GermlineCluster" ] }, { "page": "zenodoArchive", "title": "zenodoArchive", "topics": [ "zenodoArchive" ] } ], "_readme": "https://github.com/ayeletperes/piglet/raw/HEAD/README.md", "_rundeps": [ "ade4", "airr", "alakazam", "ape", "BH", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "cigarillo", "circlize", "cli", "clipr", "cluster", "codetools", "colorspace", "cpp11", "crayon", "data.table", "DBI", "DECIPHER", "dendextend", "digest", "doParallel", "dplyr", "farver", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "GlobalOptions", "glue", "gridExtra", "gtable", "gtools", "hms", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "magrittr", 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