{ "_id": "6a2299f0cd65a98ecbd57499", "Package": "Hapi", "Type": "Package", "Title": "Inference of Chromosome-Length Haplotypes Using Genomic Data of\nSingle Gamete Cells", "Version": "0.0.3", "Author": "Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong\nWei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia", "Maintainer": "Ruidong Li ", "Description": "Inference of chromosome-length haplotypes using a few\nhaploid gametes of an individual. The gamete genotype data may\nbe generated from various platforms including genotyping arrays\nand sequencing even with low-coverage. Hapi simply takes\ngenotype data of known hetSNPs in single gamete cells as input\nand report the high-resolution haplotypes as well as confidence\nof each phased hetSNPs. The package also includes a module\nallowing downstream analyses and visualization of identified\ncrossovers in the gametes.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "biocViews": "SNP, GenomicVariation, Genetics, HiddenMarkovModel,\nSingleCell, Sequencing, Microarray", "RoxygenNote": "6.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 09:38:50 UTC", "User": "root" }, "Repository": "https://rli012.r-universe.dev", "Date/Publication": "2018-07-28 14:10:07 UTC", "RemoteUrl": "https://github.com/cran/Hapi", "RemoteRef": "HEAD", "RemoteSha": "6cd2fcf8cf9753a706a6e023114ced3332602022", "MD5sum": "3f31202928f6ad262b8c592868a29bd9", "_user": "rli012", "_type": "src", "_file": "Hapi_0.0.3.tar.gz", "_fileid": "0c176822f47277bf1f5ff6d87cf8654ef8b5953c7f7b0bd53614865d455d1ad4", "_filesize": 969252, "_sha256": "0c176822f47277bf1f5ff6d87cf8654ef8b5953c7f7b0bd53614865d455d1ad4", "_created": "2026-06-05T09:38:50.000Z", "_published": 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The gamete genotype data may be generated from various platforms including genotyping arrays and next generation sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of crossovers in the gametes.", "topics": [ "Hapi-package", "Hapi" ] }, { "page": "base2num", "title": "Convert genotype coded in A/T/C/G to 0/1", "topics": [ "base2num" ] }, { "page": "crossover", "title": "Crossover information across all gamete cells", "topics": [ "crossover" ] }, { "page": "gamete11", "title": "Haplotypes of a single gamete cell for visualization", "topics": [ "gamete11" ] }, { "page": "gmt", "title": "Raw genotyping data", "topics": [ "gmt" ] }, { "page": "hapiAssemble", "title": "Consensus haplotype assembly", "topics": [ "hapiAssemble" ] }, { "page": "hapiAssembleEnd", "title": "Assembly of haplotypes in regions at the end of a chromosome", "topics": [ "hapiAssembleEnd" ] }, { "page": "hapiAutoPhase", "title": "Automatic inference of haplotypes", "topics": [ "hapiAutoPhase" ] }, { "page": "hapiBlockMPR", "title": "Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypes", "topics": [ "hapiBlockMPR" ] }, { "page": "hapiCVCluster", "title": "Filter out hetSNPs in potential complex regions", "topics": [ "hapiCVCluster" ] }, { "page": "hapiCVDistance", "title": "Histogram of crossover distance", "topics": [ "hapiCVDistance" ] }, { "page": "hapiCVMap", "title": "Visualization of crossover map", "topics": [ "hapiCVMap" ] }, { "page": "hapiCVResolution", "title": "Histogram of crossover resolution", "topics": [ "hapiCVResolution" ] }, { "page": "hapiFilterError", "title": "Filter out hetSNPs with potential genotyping errors", "topics": [ "hapiFilterError" ] }, { "page": "hapiFrameSelection", "title": "Selection of hetSNPs to form a framework", "topics": [ "hapiFrameSelection" ] }, { "page": "hapiGameteView", "title": "Visualization of haplotypes in a single gamete cell", "topics": [ "hapiGameteView" ] }, { "page": "hapiIdentifyCV", "title": "Indentify crossovers in gamete cells", "topics": [ "hapiIdentifyCV" ] }, { "page": "hapiImupte", "title": "Imputation of missing genotypes in the framework", "topics": [ "hapiImupte" ] }, { "page": "hapiPhase", "title": "Phase draft haplotypes by majority voting", "topics": [ "hapiPhase" ] }, { "page": "hg19", "title": "Chromosome information of hg19", "topics": [ "hg19" ] }, { "page": "num2base", "title": "Convert genotype coded in 0/1 to A/T/C/G", "topics": [ "num2base" ] } ], "_readme": "https://github.com/cran/Hapi/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "HMM", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "Hapi.Rmd", "filename": "Hapi.html", "title": "Hapi: an R package for chromosome-length haplotype inference using genotypic data of single gamete cells", "author": "Ruidong Li and Zhenyu Jia Department of Plant and Botany Sciences, Univeristy of California, Riverside", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Hapi 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