Package: HaploBreedR
Type: Package
Title: High-Resolution Functional Haplotype Discovery and Genomic
        Selection
Version: 0.99.1
Authors@R: 
    person("Dr. Akansha", "Singh",
           email = "akansha.iasbhu@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-4916-7296"))
Description: An end-to-end quantitative genomics and molecular breeding
        suite for crops. Identifies superior functional haplotypes from
        coding variants under false discovery rate control and conducts
        haplotype-guided genomic selection, analytical cross usefulness
        prediction, and linkage-aware pyramiding optimization.
License: MIT + file LICENSE
URL: https://aksruchi.github.io/HaploBreedR
BugReports: https://github.com/aksruchi/HaploBreedR/issues
Encoding: UTF-8
Depends: R (>= 4.4.0)
Imports: data.table (>= 1.14.0), ggplot2 (>= 3.4.0), stats, utils,
        grDevices, grid, gridExtra, gtable, methods, Biostrings (>=
        2.66.0), GenomicRanges (>= 1.50.0), IRanges (>= 2.32.0),
        rtracklayer (>= 1.58.0), boot (>= 1.3.28), withr, BEDMatrix
Suggests: ape (>= 5.6), pegas (>= 1.1), agricolae (>= 1.3.5), emmeans
        (>= 1.8), multcompView (>= 0.1.8), patchwork (>= 1.1), ggrepel
        (>= 0.9), ggbeeswarm (>= 0.7), openxlsx (>= 4.2), readxl (>=
        1.4), BiocFileCache (>= 2.6.0), BiocStyle (>= 2.26.0), knitr
        (>= 1.40), rmarkdown (>= 2.20), testthat (>= 3.1.0), future,
        future.apply
VignetteBuilder: knitr
biocViews: Software, Genetics, GenomeWideAssociation, SNP,
        GenomeAssembly, Network, PrincipalComponent, NetworkEnrichment,
        GO, FunctionalGenomics, FunctionalPrediction, GenePrediction
SystemRequirements: PLINK (>= 1.9)
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-11 10:29:50 UTC
RemoteUrl: https://github.com/BiocStaging/HaploBreedR
RemoteRef: HEAD
RemoteSha: f2e6d24e46be40f4fad35f66c94bbd64afe74abb
NeedsCompilation: no
Packaged: 2026-10-11 15:59:25 UTC; root
Author: Dr. Akansha Singh [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4916-7296>)
Maintainer: Dr. Akansha Singh <akansha.iasbhu@gmail.com>