Hapi: Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and 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 of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Version:	0.0.3
Depends:	R (≥ 3.4.0)
Imports:	HMM, ggplot2
Suggests:	knitr, testthat
Published:	2018-07-28
DOI:	10.32614/CRAN.package.Hapi
Author:	Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia
Maintainer:	Ruidong Li <rli012 at ucr.edu>
License:	GPL-3
NeedsCompilation:	no
Materials:	README NEWS
CRAN checks:	Hapi results

Documentation:

Reference manual:	Hapi.pdf
Vignettes:	'Hapi: an R/Bioconductor package for chromosome-length haplotype inference using genotypic data of single gamete cells'

Downloads:

Package source:	Hapi_0.0.3.tar.gz
Windows binaries:	r-devel: Hapi_0.0.3.zip, r-release: Hapi_0.0.3.zip, r-oldrel: Hapi_0.0.3.zip
macOS binaries:	r-release (arm64): Hapi_0.0.3.tgz, r-oldrel (arm64): Hapi_0.0.3.tgz, r-release (x86_64): Hapi_0.0.3.tgz, r-oldrel (x86_64): Hapi_0.0.3.tgz

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