Package: crosshap 1.4.0

Jacob Marsh

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>.

Authors:Jacob Marsh [aut, cre], Brady Johnston [aut], Jakob Petereit [aut]

crosshap_1.4.0.tar.gz
crosshap_1.4.0.zip(r-4.7-any)crosshap_1.4.0.zip(r-4.6-any)crosshap_1.4.0.zip(r-4.5-any)
crosshap_1.4.0.tgz(r-4.6-any)crosshap_1.4.0.tgz(r-4.5-any)
crosshap_1.4.0.tar.gz(r-4.7-any)crosshap_1.4.0.tar.gz(r-4.6-any)
crosshap_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
crosshap/json (API)

# Install 'crosshap' in R:
install.packages('crosshap', repos = c('https://bradyajohnston.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jacobimarsh/crosshap/issues

Pkgdown/docs site:https://jacobimarsh.github.io

Datasets:
  • HapObject - Example Haplotype object
  • LD - Example LD matrix
  • metadata - Example Domestication metadata
  • pheno - Example phenotype data
  • vcf - Example VCF

On CRAN:

Conda:

4.11 score 13 stars 8 scripts 361 downloads 22 exports 66 dependencies

Last updated from:c31a82bb8d. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK197
source / vignettesOK258
linux-releaseOK194
macos-releaseOK190
macos-oldrelOK166
windows-develOK162
windows-releaseOK158
windows-oldrelOK169
wasm-releaseOK165

Exports:%>%arith_modebuild_bot_halfeyeplotbuild_left_alleleplotbuild_left_posplotbuild_mid_dotplotbuild_right_clusterplotbuild_right_phenoplotbuild_summary_tablesbuild_top_metaplotclustree_vizcrosshap_vizmean_na.rmprepare_hap_umappseudo_hapsread_LDread_metadataread_phenoread_vcfrun_haplotypingrun_hdbscan_haplotypingtagphenos

Dependencies:backportsbase64enccachemcheckmatecliclustreecpp11data.tabledbscandistributionaldplyrfarverfastmapgenericsggdistggforceggplot2ggppggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmemoisenumDerivpatchworkpillarpkgconfigpolyclippolynompurrrquadprogR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttimechangetweenrutf8vctrsviridisviridisLitewithrxtszoo