Package: crosshap 1.4.0

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]

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crosshap/json (API)

Peer review:

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

On CRAN:

22 exports 11 stars 1.65 score 69 dependencies 4 scripts 329 downloads

Last updated 6 months agofrom:69b407bb80. Checks:OK: 7. Indexed: yes.

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:backportscachemcheckmatecliclustreecolorspacecpp11data.tabledbscandistributionaldplyrfansifarverfastmapgenericsggdistggforceggplot2ggppggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmunsellnlmenumDerivpatchworkpillarpkgconfigpolyclippolynompurrrquadprogR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttimechangetweenrutf8vctrsviridisviridisLitewithrxtszoo