crosshap: Local Haplotype Clustering and Visualization

A local haplotyping visualization toolbox to capture major patterns of co-inheritance between clusters of linked variants, whilst connecting findings to phenotypic and demographic traits across individuals. 'crosshap' enables users to explore and understand genomic variation across a trait-associated region. For an example of successful local haplotype analysis, see Marsh et al. (2022) <doi:10.1007/s00122-022-04045-8>.

Version: 1.4.0
Depends: R (≥ 4.00)
Imports: cli, clustree, data.table, dbscan, dplyr, ggdist, ggplot2, ggpp, gridExtra, gtable, magrittr, patchwork, rlang, scales, tibble, tidyr
Suggests: covr, knitr, rmarkdown, testthat (≥ 3.0.0), umap, vdiffr
Published: 2024-03-31
Author: Jacob Marsh ORCID iD [aut, cre], Brady Johnston ORCID iD [aut], Jakob Petereit ORCID iD [aut]
Maintainer: Jacob Marsh <jake.marsh at live.com.au>
BugReports: https://github.com/jacobimarsh/crosshap/issues
License: MIT + file LICENSE
URL: https://jacobimarsh.github.io/crosshap/
NeedsCompilation: no
Materials: README
CRAN checks: crosshap results

Documentation:

Reference manual: crosshap.pdf

Downloads:

Package source: crosshap_1.4.0.tar.gz
Windows binaries: r-devel: crosshap_1.4.0.zip, r-release: crosshap_1.4.0.zip, r-oldrel: crosshap_1.4.0.zip
macOS binaries: r-release (arm64): crosshap_1.4.0.tgz, r-oldrel (arm64): crosshap_1.4.0.tgz, r-release (x86_64): crosshap_1.4.0.tgz
Old sources: crosshap archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=crosshap to link to this page.