{ "_id": "6acca7bfa14063b82c3a772a", "Package": "MHCtools", "Type": "Package", "Title": "Analysis of MHC Data in Non-Model Species", "Version": "1.6.0", "Authors@R": "person(\"Jacob\", \"Roved\", email = \"jacob.roved@biol.lu.se\", \nrole = c(\"aut\", \"cre\"))", "Description": "Sixteen tools for bioinformatics processing and analysis\nof major histocompatibility complex (MHC) data. The functions\nare tailored for amplicon data sets that have been filtered\nusing the dada2 method (for more information on dada2, visit\n ), but even other types of\ndata sets can be analyzed. The ReplMatch() function matches\nreplicates in data sets in order to evaluate genotyping\nsuccess. The GetReplTable() and GetReplStats() functions\nperform such an evaluation. The CreateFas() function creates a\nfasta file with all the sequences in the data set. The\nCreateSamplesFas() function creates individual fasta files for\neach sample in the data set. The DistCalc() function calculates\nGrantham, Sandberg, or p-distances from pairwise comparisons of\nall sequences in a data set, and mean distances of all pairwise\ncomparisons within each sample in a data set. The function\nadditionally outputs five tables with physico-chemical\nz-descriptor values (based on Sandberg et al. 1998) for each\namino acid position in all sequences in the data set. These\ntables may be useful for further downstream analyses, such as\nestimation of MHC supertypes. The BootKmeans() function is a\nwrapper for the kmeans() function of the 'stats' package, which\nallows for bootstrapping. Bootstrapping k-estimates may be\ndesirable in data sets, where e.g. BIC- vs. k-values do not\nproduce clear inflection points (\"elbows\"). BootKmeans()\nperforms multiple runs of kmeans() and estimates optimal\nk-values based on a user-defined threshold of BIC reduction.\nThe method is an automated and bootstrapped version of visually\ninspecting elbow plots of BIC- vs. k-values. The ClusterMatch()\nfunction is a tool for evaluating whether different k-means()\nclustering models identify similar clusters, and summarize\nbootstrap model stats as means for different estimated values\nof k. It is designed to take files produced by the BootKmeans()\nfunction as input, but other data can be analyzed if the\ndescriptions of the required data formats are observed\ncarefully. The SynDist() function analyses of synonymous\nvariation among aligned protein-coding DNA sequences, that is,\nnucleotide substitutions that do not translate to changes in\nthe amino acid sequences due to degeneracy of the genetic code.\nThe SynDist() function calculates synonymous nucleotide changes\nper base and per codon in pairwise sequence comparisons, as\nwell as mean synonymous variation among all pairwise\ncomparisons of the sequences within each sample in a data set.\nThe PapaDiv() function compares parent pairs in the data set\nand calculate their joint MHC diversity, taking into account\nsequence variants that occur in both parents. The HpltFind()\nfunction infers putative haplotypes from families in the data\nset. The GetHpltTable() and GetHpltStats() functions evaluate\nthe accuracy of the haplotype inference. The\nCreateHpltOccTable() function creates a binary (logical)\nhaplotype-sequence occurrence matrix from the output of\nHpltFind(), for easy overview of which sequences are present in\nwhich haplotypes. The HpltMatch() function compares haplotypes\nto help identify overlapping and potentially identical types.\nThe NestTablesXL() function translates the output from\nHpltFind() to an Excel workbook, that provides a convenient\noverview for evaluation and curating of the inferred putative\nhaplotypes.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 09:22:01 UTC", "User": "root" }, "Author": "Jacob Roved [aut, cre]", "Maintainer": "Jacob Roved ", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://jr-evolecol.r-universe.dev", "Date/Publication": "2026-02-14 17:20:02 UTC", "RemoteUrl": "https://github.com/cran/MHCtools", "RemoteRef": "HEAD", "RemoteSha": "42e087db5a3e34abf50edc8ce321503e650ebaa4", "_user": "jr-evolecol", "_type": "src", "_file": "MHCtools_1.6.0.tar.gz", "_fileid": "https://r2.ropensci.org/219f10a3dbe27ac8a7b75993fa9e0137ef13cad62f434d30dbb29bea63944b34", "_filesize": 316114, "_sha256": "219f10a3dbe27ac8a7b75993fa9e0137ef13cad62f434d30dbb29bea63944b34", "_expires": "2027-01-20T09:26:21.000Z", "_created": "2026-10-12T09:22:01.000Z", "_published": "2026-10-12T09:26:23.370Z", "_buildurl": "https://github.com/r-universe/jr-evolecol/actions/runs/38229136261", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114745096524, "time": 140, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11737293921" }, { "job": 114745096565, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11737508531" }, { "job": 114745096560, "time": 175, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11738326797" }, { "job": 114745096542, "time": 195, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11737772484" }, { "job": 114744088705, "time": 164, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11737118629" }, { "job": 114745096550, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11738201907" }, { "job": 114745096658, "time": 131, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11737753291" }, { "job": 114745096581, "time": 76, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11737488501" }, { "job": 114745096590, "time": 102, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11737039191" } ], "_upstream": "https://github.com/cran/MHCtools", "_commit": { "id": "42e087db5a3e34abf50edc8ce321503e650ebaa4", "author": "Jacob Roved ", "committer": "cran-robot ", "message": "version 1.6.0\n", "time": 1771089602 }, "_maintainer": { "name": "Jacob Roved", "email": "jacob.roved@biol.lu.se", "login": "jr-evolecol", "description": "Researcher (PhD) in ecology and evolutionary biology, special interests are immunogenetics and sexual conflict.", "uuid": 31538178 }, "_distro": "resolute", 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"date": "2025-01-17" }, { "version": "1.5.5", "date": "2025-01-18" }, { "version": "1.6.0", "date": "2026-02-16" } ], "_exports": [ "BootKmeans", "ClusterMatch", "CreateFas", "CreateHpltOccTable", "CreateSamplesFas", "DistCalc", "GetHpltStats", "GetHpltTable", "GetReplStats", "GetReplTable", "HpltFind", "HpltMatch", "NestTablesXL", "PapaDiv", "ReplMatch", "SynDist" ], "_datasets": [ { "name": "hplt_occurrence_matrix", "title": "Data hplt_occurrence_matrix", "object": "hplt_occurrence_matrix", "class": [ "data.frame" ], "fields": [ "Sequence_001", "Sequence_002", "Sequence_003", "Sequence_004", "Sequence_005", "Sequence_006", "Sequence_007", "Sequence_008", "Sequence_009", "Sequence_010", "Sequence_011", "Sequence_012", "Sequence_013", "Sequence_014", "Sequence_015", "Sequence_016", "Sequence_017", "Sequence_018", "Sequence_019", "Sequence_020", "Sequence_021", "Sequence_022", "Sequence_023", "Sequence_024", "Sequence_025", "Sequence_026", "Sequence_027", "Sequence_028", "Sequence_029", 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"class": [ "data.frame" ], "fields": [ "Sample_ID", "Replic_set" ], "rows": 111, "table": true, "tojson": true }, { "name": "sequence_table", "title": "Data sequence_table", "object": "sequence_table", "class": [ "data.frame" ], "fields": [], "rows": 334, "table": true, "tojson": true }, { "name": "sequence_table_fas", "title": "Data sequence_table_fas", "object": "sequence_table_fas", "class": [ "data.frame" ], "fields": [ "ATGAGATCGTGAGGCTACCCTCACACTAGACGTTTCGGTA", "TCTTGTGGTCTGCTATGACCGCAGTGAATCGAAGACCAAC", "AAGCCCTGTATTAGTCCTTGTACGGAAGGATGAATCGCCC", "CTGTACTATTCCCTAGACGAACGTTAATTGCGGCAGGCGA", "AGCCGGACTCGACGTTCGTATGAGGATGCTTTACTAACCA", "GAATTGCCAGCTCAGGTGCGTAATACTTCGAAGTGCACTC", "TCAATAAAACCTAAGGCTCCTACGTACCGTTGCTGGGTGG", "GCCCAAGCGTACCGTGTTGGTAGCCTTAATAGAATCGACT", "ATTAGATGTGACCGTCCCTCGACTAGTGGCGAACGTCATA", "CCCTATCATGTGTCAACGAGCGGGAATGTTAAGCCTACTG", "ATACGCCCGTTTGAGACGTCTTAAAGGTGACAGCATCTGC", "CATGCAAAGTTCCCTGGATCCCAAGAACGTTATGGTGTGC", "TTATTTCCAGGCTAAGGAGCGCGCGGTCAGTCACTATCAA", "TTAGGCAACTGCACTCACGTACTTGGGTAGCATAACCGGT", "CTTTCTTAAGAGGGTTCACGCTGACCGAGGACGAACACTT", "GTTAGACTCGGTAGGCGGAGTCTACCGACATCCCTAAATT", "ATTGCAAAGCGCGGAACCCCGTCTTCTTAAATCGTGGTGA", "TGGTAATCGACAGGCTGAACTTCAACCGTCCAACGGGTTT", "TTACGCTAAGCAGGAGGCGTTGTAGACGCATTACACTCCT", "CGAAATCTGCCTCCTAAAGAACGTATGCGCGTGTTCTGAG", "AGGGACCCTCTCATGGTCAAAGTTTCAGTAGAGGTTCACC", "TGGCGGTAAACTCACTCTTCAACACGCGTGTCTAAAGTGG", "AGTCGATATGAAGCGTTCTCTCGATTCCCTACAGACGGAG", "CGTGGAAACCATAGCCCAGTTCCTGATCATTATGCAGGTG", "TAAGCGTATCTACGTTGCCTCAAGCGCTAAAGGCACGTTG", "CATTACTCGGAGCCAGGATGTTTCGAGCACCCTATGAAGT", "GCATAAATCACCTTGTGCTCGTCGTGAGTAATCAGGGCAC", "TGGCACCCATTATCGAGTCGGATTAGAAAGCGGTCCTCAT", "AGATCGACGTAACACCCAGTGCGTATCGGTTCTTCAAGGT", "GTCAAGTTCAATCCGTCACCTGGTGCTGCTAAAGGTCGAA", "TATCCTAGCGTTAATAACGAAGGCGGTCAAGCCTTGTCGC", "TACATCCACGAGCATCTGCTTCGGTGTACCGAAAGAGGTT", "CTGGACAAAGTACGGACCGATTCTGCTCATAGCTTGTCAG", "TACAGGCTGTCCATAGTACATAGTCCGTAGCGAGTCCGAT", "TAAACGACTCATTCCGGCGGGCATGAGGCAGTTTCTTAAC", "ACTCCAACGTTACTACCGAGAGGGAATCTTTGCTAGCGTG", "ATATCGCGAGGCGATACATGCCGTAGGTGTTCACTCTACA", "GTGTAATGACCCCGATAGAGCTCATTATGCATAGGTGCCC", "TTGCGCTCGGCGATGACGCCTACGAATGTGATAAACTCTA", "TATGCGTCAAGTACCTATGGTAGCCTAGAACATCGGGCCT", "TCCAAATGGGCCGGTGTTTAGACTCATCGCTGACTAGACA", "TATACGCAAGCCGTACTTCTCATGAGATGCGGTGCAATGC", "AACGCAATGTACCAGTTTCTGCTGTAATCATCCCGGGGGA", "ATTAGCGCGTAGTATCGCCGATACGACGGCCCAAAGTTTT", "TAGTCCTGCGAAAAGGCTATCCGTGTAAGCCCAGTCAGTT", "CGTGTCGATATGGAGTCACAACCATTGGCCACTTAGGCTA", "TCATACCGATGGGTCCTAGTAAGTACCTAGACAGGGCCTT", "CGATTCTCCCTCCGTTAGGAGGATAAAATTCCGGGAATCG", "AATATACACGGCTACATGTGCGGTAGACCTGGTCCGTTAC", "ATTTGAAATAACTCAACGTACGCTGTCGGGCGCGTACTCG", "AATTCGCGGACACTCTTCTGATCGAGAGGCATCAATGGCT", "TTATTGTAGAATTTTTAGCGGGCCAGGCCACCCGAGACCA", "AATGATCAGACCCTTGCCGGCATTGTGTGCAATCGAACTG", "GTGGGCGAATACTCCTCCAGACGTGTATCCTGAAATACTG", "TACTGCTCCGCATGGTGATGAGCACTGGCGAACTACAATT", "AATTATGGCATCGGATGCCCAGTATTCGGCAAGTCCATCG", "CTGATGAATTGCCAGTGAAATTGCGGCGTTCGACCCACAT", "GTTGCTAACCTATTCAACGCGCCTCGGAGATGATGAGCAT", "GCTGTCTCCATATGATGCGTCACGATAGCGTAAATCCAGG", "CCATGGTCATTTGTCCAAGCTACTAACGTAGAGTGACGGC", "ATGTAGATCGTATAAACCGAACCCGGTCTTGTCGGCTGCA", "CGCTTAGGTCCTACACAGGTAGCTTGTAATACACGCAGTG", "TTACGTGCCGATCGACGTCTACTGCACGCATAGGTTAAAG", "CCCTGCCTCGTACGGAGCTTAGAGATGGCTAGTAACATTA", "CGGGGTCCCAATGGGTGAATCAATCCAACCTAGGATTTTC", "CGTCTCGGTATAGAAATCATGTCGCAGCGTCGCTACATAG", "GGCGCACTCTTTCCAGCTTAGTGGGTAGTTCCAGAAAAAC", "CTTAATCTCGCTACGCGGGTAACCCTTGAATGGAGTACGA", "TAAATAGCCTAGGTCGTTATGGACCGGATCAGCCACTGCT", "GCTTATATGGATCACAAATTTCTCGTAACCGCGCAGGGGC", "TCGTTTAAAATTTGCCGAGGCATATAGCGCGCTCAGGACC", "ACCAGAGTGTTAGCCCCAAAGATTATGTGGCGCTCTCGAT", "TCACCGCCTCGCTCTTAGAGAGAATGGACGGTTAACTTAG", "GCTCTTCATCCATCGTAAAGATAATGTACTGGCCCGAGGG", "TCGCCGACCGGAGATGTACATGTTTGGGAAATCCTTCACA", "ACCTTCTATCGATTCCTCGTAGGATAGGAACACGGGAGCT", "CTATAATACTAGACCGTCCACTGCGGGAGGGTTTCACATG", "GAAGATTATCGCGGTGTAAAGTCAATCGTAGCTCGCCCCT", "GACCGACATACGCGGCACGTTTTCAGGGATTAACGCATTT", "ATGTATCTCTAGAATCTAACGCTACCCCTGAGGAGGGCGT", "AAGGCGCGAACTGTCTAACTCGGCTCTGATATATGTCCGA", "GCCAGCAATGCGTATGACGGATATTGTACGTGCTCCTACA", "AACCCGCTGGTGATGCGCCATTGGCCGATAAATATCTTAG", "TCGTGCTACAACTCTTAGTAGCCCGAGATTGAGCCGGAAT", "CTGAGGCCACGGTAACTTTGTCCAACGAACCGATTTAGTG", "GTGACCAACACCTACCTGACTATGTGGTAGTAGCCATTGG", "GAAGAAAAGTAGCGACACTCTGATCCGGTCTGCTTGTCCT", "TACGCTGATGATGGTCACTTAGACTGGGAACTACCGCCTA", "TACTGTTGTTGAAAACGACGAGGACCGTAGCGCCATTCTC", "CAGGATTCCGACTGACTAGTAATTGAACTAGGGCCTTCCG", "GCAAGCGGTTATGTCAGTCCCTAATAAAGAGCTCCTGCTG", "ACCAAAGAGGGGCCTAGTGAATGCATATTTCCTGCGCTCT", "CAGCCCACTTCAGGAGGCTAGGGTATTGCAATTATAGCCT", "CCTAGTCCATCGACTGCTTGCTAAGGGTACAGGCTGATAA", "TAGAGTCTCACGTAAGGTGCCCTTGGAACTTCTCGCAGAA", "TTTAACTCATATACAACTGTGGCACCCCGTGGGGGATAGC", "TATCGGGCCGCCTCACAGTTAACTGCACGATTAGATGATG", "ACGCACTTCATCGGGGTCAACCAGAGTAAGTGTCGATCTT", "TAATTCACCTCCGGCGTCCAATTTGGTCCGTGAAGAGAGA", "CCTGCACGCAGTGCATCGTGAGTTTACACTAAGTCAGGAT", "GCTTGTTGGTCGGTCCATGAAAACAGGACTTGCTCACCAA", "GCCTGACGACGCCAGGTGTGGCACGTTCTAAATACTTTAA", "ATGAATTTTACGAGACGCTGCATGCACCCTGTCCGAGTGA", "ATCGAGGTTCCCAGTGTCCACTTACGAAGCGCTAGATAGT", "CTAACACTGCAGTATATCAGCGGGCCTATATCAGTCGGGT", "GAACTGATGGGCTACAACCTTCTCTAATGTAGGCCGAGTC", "TATCCTTGCCAGCGGTGATACACGCGAGAAATTTCGCGAT", "TGAAAAGGAGCACTCCGTACTCCTGGAATTTTTCCGGGAC", "AGTACGCGATTGGACTCGACCGAGGCTAATTACATTCTGC", "GAGCTCCGGGCGAATAATTCTAGCCATTGATTGGTCCACA", "CATAGAGTGAAGGATGGCTGATTCAAACCCGTCGTTCTCC", "CCCCAGAGCTAGCAATGTCTGCAGCTGATTTGGACTTGAA", "ATTCCAGTTCGAACGGAGGCTTGGTTCCACCTGAAATACG", "GTGCTTAATGAGGCACAGGATCTAACGACCTCCGTTGATC", "TTCCATCAGCACGTTGAGGCGACATTGGACGTCATATGCA", "GGAACACGTTATTAGTGAGACGCTACGGCTTGCACTCCAT", "GTGCATTAACTTTAGCCATTCCGACTCTGGAGCAAGCGAG", "CCCATCACCGCATTGTCGTCGCATGTGAATAGTAAGTGGA", "CCTGCCATGGTAGACACTCCATTAGATGGGGATCTAATGC", "GAACAGAGGGGAATACTTTTGCCACGACCGTTCATGTCCT", "ACCACTAGACTTTAAGCGTAATCGCCGCTTGCGGGTTAAG", "CATGCCGGACTATAGAGTTATGGCTCGGATTACCATGACC", "TAGTCAATCCGAGCGTCGTACGATCGATCAACCGTTGTGA", "CGCCTGATATCCTAAGCGTGGCGGTAAACTGTCTGATCAA", "AGATTACGGGATTGTCCTCGCATACATAGCATCGGCCTGA", "TGTCCCCGCCTTCCGTTTAAAAAGGAGTCGAGGTCAAAGT", "ATGCCTCAGGCTTGTACCACCGAAGGAATTGTCTTGGACA", "TGTACTAGGTAGCACTTAGTGCGCAGTCCCAATACTGCGA", "GCAGCTATGCTGCCGACAGGTCTTATAGGACTGCTTACAA", "TCCTTGGAACGGCCCCTCTGTATAGGAACTAGATGATACG", "TATGCCCTCGGTACATAACTGACGATGACGTGAGGTTCCA", "GTGGTCGCTGTTACATAGTGAGAGCACTCCTAAGCCTCAA", "TGCCGGCTCTGTACCGGGCACTTGAATAAAGATCATGATC", "ATGCGCCCACTGATTGCCGTGCCAATGACATTGTGATAAG", "TGGTTCTCGAGGCTTAAACCGAGATCTGATCAACTAGGCC", "GAATAATGCGTAACCGATCTCAGACTCAGTGTTCCGGGTC", "GCGACGAAAGGAGTCAACGCATAGCCGTCTTTATTTCTCG", "TCGAATAAGCCCGAACTACCCTTTTTGGACAAGGCGGTGT", "GTCTCTGCGCGATGGCTCGGTATAGCACAATATAGCACTA", "AAACATCGTATACGAGGCGTAGCCTTACGGTGCTGACTTC", "TCGCAATGTTACGCATATTGGCACCGCATGCTAGGTCAAG", "TGATCCGAATTATGCATGCTGTGACCATGGCGCACCAGAT", "ACAGGCTTGATCCGAGTTGCAATGCGGTCTGCACCAATTA", "CACTAAACGTTCCCTGATGCTCTGAGAGTCTGTACGGAGA", "CATAAGTTCTAGATCGTCGCTGCCCAACGAGGAATGTTGC", "ATTGTGACATACATCGGAGGCGCCCTTACCAATTGGGATC", "CAAGTCAGTACATGCACGCGATATCCTAGTGGTCCGTATG", "CGCCGGAATTAGGGTACATGTCTTCGCTAACTTGCAAAGC", "CTGCGTATTGACATAAAGGTCCTTTGGCTAACGCGGCCAA", "CCGGTCCAGTAGCGATTTGTACAGCGATTGAATGCATCCA", "AGATGCGCCCATCGTGACCTTCAAATTATGTGGTGACCAG", "GCGAAACTGTTGGAACTGCCTCCAATGGATGAATTCCGCT", "GATACTATTTCATTGAGGAGCCACCCCTCGAGGTCGGAAT", "CATGTTACATAACCGTATCGCTAGACGCTGGCGTTAGAGC", "AGAACCGCGGCCTATTGAGATCTTCATCTTCTAAGCGGGA", "AGCCCTAGTTTCGGAGGATCCTTAAACTAGAGCCCGTTAG", "TTTCACGGGAGCCAACAAGAGTTCATGACTTCGTTCCGGA", "TCGCGTACCGACAAACTGTTCTTAGGCCATCATAGAGGGT", "TCTACTGCAATGCTTCCTTCGTCAAAAGACGTGGGGGAAC", "GGGAAGGGATCCTATTGCAATGTCCTCAATCCCATTGGAC", "CATAGGCTGTAAATTGACCTACAGGCGAGTCATTCCGTGC", "TGCTCGCTACTGGATCCCGAACTAATAATGTCGAAGTCGG", "TTAATTCGCCACGTAGCAGGATGGGAGTGTCCCCACTTAA", "TGTCACGTAACAGCTGCCTCATAATGGGACTATGGTCAGC", "CACCATCCGGCAAGGATGCGTATTTCTTTCGTGAGCAAAG", "AACCGCTGGGGAAGGTTCGGACACAATCTACTTCACTTTG" ], "rows": 100, "table": true, "tojson": true }, { "name": 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