The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
Haplotype calling from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers. The package was first described in Bioinformatics by Utsunomiya et al. (2016, <doi:10.1093/bioinformatics/btw356>). Since the v2 release, the package provides functions for unsupervised and supervised detection of ancestry tracks. The methods implemented in these functions were described in an article published in Methods in Ecology and Evolution by Utsunomiya et al. (2020, <doi:10.1111/2041-210X.13467>). The source code for v3 was modified for improved performance and inclusion of new functionality, including analysis of unphased data, runs of homozygosity, sampling methods for virtual gamete mating, mixed model fitting and GWAS.
| Version: | 3.0.0 |
| Imports: | parallel (≥ 3.4.4), Matrix (≥ 1.2-16), methods (≥ 3.4.4), pedigreemm (≥ 0.3-3), sparseinv (≥ 0.1.3), e1071 (≥ 1.7-0.1), class (≥ 7.3-15), data.table (≥ 1.12.6), stringi (≥ 1.7.6) |
| Suggests: | R.rsp |
| Published: | 2022-07-01 |
| DOI: | 10.32614/CRAN.package.GHap |
| Author: | Yuri Tani Utsunomiya, Andre Vieira do Nascimento, Marco Milanesi, Mario Barbato |
| Maintainer: | Yuri Tani Utsunomiya <ytutsunomiya at gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Citation: | GHap citation info |
| CRAN checks: | GHap results |
| Reference manual: | GHap.pdf |
| Vignettes: |
GHap vignette |
| Package source: | GHap_3.0.0.tar.gz |
| Windows binaries: | r-devel: GHap_3.0.0.zip, r-release: GHap_3.0.0.zip, r-oldrel: GHap_3.0.0.zip |
| macOS binaries: | r-release (arm64): GHap_3.0.0.tgz, r-oldrel (arm64): GHap_3.0.0.tgz, r-release (x86_64): GHap_3.0.0.tgz, r-oldrel (x86_64): GHap_3.0.0.tgz |
| Old sources: | GHap archive |
Please use the canonical form https://CRAN.R-project.org/package=GHap to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.