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 |
| 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-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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