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
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

Downloads:

Reference manual: Hapi.pdf
Vignettes: 'Hapi: an R/Bioconductor package for chromosome-length haplotype inference using genotypic data of single gamete cells'
Package source: Hapi_0.0.3.tar.gz
Windows binaries: r-devel: Hapi_0.0.3.zip, r-devel-gcc8: Hapi_0.0.3.zip, r-release: Hapi_0.0.3.zip, r-oldrel: Hapi_0.0.3.zip
OS X binaries: r-release: Hapi_0.0.3.tgz, r-oldrel: Hapi_0.0.3.tgz

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