{ "_id": "6a1d480e1d7bb097a0a42797", "Package": "adegenet", "Title": "Exploratory Analysis of Genetic and Genomic Data", "Version": "2.1.11", "Authors@R": "c(person(given = \"Thibaut\",\nfamily = \"Jombart\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-2226-8692\")),\nperson(given = \"Zhian N.\",\nfamily = \"Kamvar\",\nrole = c(\"aut\", \"cre\"),\nemail = \"zkamvar@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1458-7108\")),\nperson(given = \"Caitlin\",\nfamily = \"Collins\",\nrole = \"ctb\"),\nperson(given = \"Roman\",\nfamily = \"Lustrik\",\nrole = \"ctb\"),\nperson(given = \"Marie-Pauline\",\nfamily = \"Beugin\",\nrole = \"ctb\"),\nperson(given = \"Brian J.\",\nfamily = \"Knaus\",\nrole = \"ctb\"),\nperson(given = \"Peter\",\nfamily = \"Solymos\",\nrole = \"ctb\"),\nperson(given = \"Vladimir\",\nfamily = \"Mikryukov\",\nrole = \"ctb\"),\nperson(given = \"Klaus\",\nfamily = \"Schliep\",\nrole = \"ctb\"),\nperson(given = \"Tiago\",\nfamily = \"Maié\",\nrole = \"ctb\"),\nperson(given = \"Libor\",\nfamily = \"Morkovsky\",\nrole = \"ctb\"),\nperson(given = \"Ismail\",\nfamily = \"Ahmed\",\nrole = \"ctb\"),\nperson(given = \"Anne\",\nfamily = \"Cori\",\nrole = \"ctb\"),\nperson(given = \"Federico\",\nfamily = \"Calboli\",\nrole = \"ctb\"),\nperson(given = \"RJ\",\nfamily = \"Ewing\",\nrole = \"ctb\"),\nperson(given = \"Frédéric\",\nfamily = \"Michaud\",\nrole = \"ctb\"),\nperson(given = \"Rebecca\",\nfamily = \"DeCamp\",\nrole = \"ctb\"),\nperson(given = \"Alexandre\",\nfamily = \"Courtiol\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0637-2959\")),\nperson(given = \"Lindsay V.\",\nfamily = \"Clark\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3881-9252\")),\nperson(given = \"Pavel\",\nfamily = \"Dimens\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3823-0373\")),\nperson(given = \"Max\",\nfamily = \"Coulter\",\nrole = \"ctb\"),\nperson(given = \"Ivan\",\nfamily = \"Krylov\",\nrole = \"ctb\")\n)", "Description": "Toolset for the exploration of genetic and genomic data.\nAdegenet provides formal (S4) classes for storing and handling\nvarious genetic data, including genetic markers with varying\nploidy and hierarchical population structure ('genind' class),\nalleles counts by populations ('genpop'), and genome-wide SNP\ndata ('genlight'). 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Kamvar [aut, cre] (ORCID:\n),\nCaitlin Collins [ctb],\nRoman Lustrik [ctb],\nMarie-Pauline Beugin [ctb],\nBrian J. Knaus [ctb],\nPeter Solymos [ctb],\nVladimir Mikryukov [ctb],\nKlaus Schliep [ctb],\nTiago Maié [ctb],\nLibor Morkovsky [ctb],\nIsmail Ahmed [ctb],\nAnne Cori [ctb],\nFederico Calboli [ctb],\nRJ Ewing [ctb],\nFrédéric Michaud [ctb],\nRebecca DeCamp [ctb],\nAlexandre Courtiol [ctb] (ORCID:\n),\nLindsay V. Clark [ctb] (ORCID: ),\nPavel Dimens [ctb] (ORCID: ),\nMax Coulter [ctb],\nIvan Krylov [ctb]", "Maintainer": "Zhian N. 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genlight objects", "topics": [ "glSim" ] }, { "page": "H3N2", "title": "Seasonal influenza (H3N2) HA segment data", "topics": [ "H3N2", "USflu", "usflu", "USflu.fasta", "usflu.fasta" ] }, { "page": "haploGen", "title": "Simulation of genealogies of haplotypes", "topics": [ "as.igraph.haploGen", "as.POSIXct.haploGen", "as.seqTrack.haploGen", "haploGen", "haploGen-class", "labels.haploGen", "plot.haploGen", "plotHaploGen", "print.haploGen", "sample.haploGen", "seqTrack.haploGen", "[.haploGen" ] }, { "page": "hierarchy-methods", "title": "Access and manipulate the population hierarchy for genind or genlight objects.", "topics": [ "hier", "hier,genind-method", "hier,genlight-method", "hier<-", "hier<-,genind-method", "hier<-,genlight-method" ] }, { "page": "Hs", "title": "Expected heterozygosity (Hs)", "topics": [ "Hs" ] }, { "page": "Hs.test", "title": "Test differences in expected heterozygosity (Hs)", "topics": [ "Hs.test" ] }, { "page": "HWE", "title": "Hardy-Weinberg Equilibrium test for multilocus data", "topics": [ "HWE.test.genind" ] }, { "page": "hybridize", "title": "Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.", "topics": [ "hybridize" ] }, { "page": "hybridtoy", "title": "Toy hybrid dataset", "topics": [ "hybridtoy" ] }, { "page": "import2genind", "title": "Importing data from several softwares to a genind object", "topics": [ "import2genind" ] }, { "page": "inbreeding", "title": "Likelihood-based estimation of inbreeding", "topics": [ "inbreeding" ] }, { "page": "new.genind", "title": "genind constructor", "topics": [ "as.genind", "genind", "initialize,genind-method", "initialize,genind-methods" ] }, { "page": "new.genpop", "title": "genpop constructor", "topics": [ "as.genpop", "genpop", "initialize,genpop-method", "initialize,genpop-methods" ] }, { "page": "isPoly", "title": "Assess polymorphism in genind/genpop objects", "topics": [ "isPoly", "isPoly,genind-method", "isPoly,genpop-method", "isPoly-methods" ] }, { "page": "KIC", "title": "Compute Akaike Information Criterion for small samples (AICc) for snapclust", "topics": [ "KIC", "KIC.snapclust" ] }, { "page": "loadingplot", "title": "Represents a cloud of points with colors", "topics": [ "loadingplot", "loadingplot.default" ] }, { "page": "makefreq", "title": "Compute allelic frequencies", "topics": [ "makefreq", "makefreq,genind-method", "makefreq,genind-methods", "makefreq,genpop-method", "makefreq,genpop-methods", "makefreq.genind", "makefreq.genpop" ] }, { "page": "microbov", "title": "Microsatellites genotypes of 15 cattle breeds", "topics": [ "microbov" ] }, { "page": "minorAllele", "title": "Compute minor allele frequency", "topics": [ "minorAllele" ] }, { "page": "monmonier", "title": "Boundary detection using Monmonier algorithm", "topics": [ "monmonier", "optimize.monmonier", "plot.monmonier", "print.monmonier" ] }, { "page": "nancycats", "title": "Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)", "topics": [ "nancycats" ] }, { "page": "old2new", "title": "Convert objects with obsolete classes into new objects", "topics": [ "old2new", "old2new_genind", "old2new_genlight", "old2new_genpop" ] }, { "page": "pairDist", "title": "Pairwise distance plots", "topics": [ "pairDist", "pairDist.default", "pairDistPlot", "pairDistPlot.default", "pairDistPlot.dist", "pairDistPlot.DNAbin", "pairDistPlot.genind", "pairDistPlot.matrix" ] }, { "page": "propShared", "title": "Compute proportion of shared alleles", "topics": [ "propShared" ] }, { "page": "propTyped", "title": "Compute the proportion of typed elements", "topics": [ "propTyped", "propTyped,genind-method", "propTyped,genpop-method", "propTyped-methods" ] }, { "page": "read.fstat", "title": "Reading data from Fstat", "topics": [ "read.fstat" ] }, { "page": "read.genepop", "title": "Reading data from Genepop", "topics": [ "read.genepop" ] }, { "page": "read.genetix", "title": "Reading data from GENETIX", "topics": [ "read.genetix" ] }, { "page": "read.snp", "title": "Reading Single Nucleotide Polymorphism data", "topics": [ "read.snp" ] }, { "page": "read.structure", "title": "Reading data from STRUCTURE", "topics": [ "read.structure" ] }, { "page": "repool", "title": "Pool several genotypes into a single dataset", "topics": [ "repool" ] }, { "page": "rupica", "title": "Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)", "topics": [ "rupica" ] }, { "page": "scaleGen", "title": "Compute scaled allele frequencies", "topics": [ "scaleGen", "scaleGen,genind-method", "scaleGen,genpop-method", "scaleGen-methods" ] }, { "page": "selpopsize", "title": "Select genotypes of well-represented populations", "topics": [ "selPopSize", "selPopSize,ANY-method", "selPopSize,genind-method", "selPopSize-methods" ] }, { "page": "seploc", "title": "Separate data per locus", "topics": [ "seploc", "seploc,ANY-method", "seploc,genind-method", 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"showmekittens" ] }, { "page": "sim2pop", "title": "Simulated genotypes of two georeferenced populations", "topics": [ "sim2pop" ] }, { "page": "snapclust", "title": "Maximum-likelihood genetic clustering using EM algorithm", "topics": [ "snapclust" ] }, { "page": "snapclust.choose.k", "title": "Choose the number of clusters for snapclust using AIC, BIC or AICc", "topics": [ "snapclust.choose.k" ] }, { "page": "SNPbin", "title": "Formal class \"SNPbin\"", "topics": [ "$,SNPbin-method", "$<-,SNPbin-method", "as,integer,SNPbin-method", "as,numeric,SNPbin-method", "as.integer.SNPbin", "c.SNPbin", "cbind.SNPbin", "coerce,SNPbin,integer-method", "initialize,SNPbin-method", "NA.posi,SNPbin-method", "names,SNPbin-method", "nLoc,SNPbin-method", "ploidy,SNPbin-method", "ploidy<-,SNPbin-method", "show,SNPbin-method", "SNPbin", "SNPbin-class", "[,SNPbin,ANY,ANY,ANY-method", "[,SNPbin,ANY,ANY-method", "[,SNPbin-method" ] }, { "page": "snpposi", "title": "Analyse the position of polymorphic sites", 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