Package: HaploBreedR 0.99.1

Dr. Akansha Singh

HaploBreedR: High-Resolution Functional Haplotype Discovery and Genomic Selection

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.

Authors:Dr. Akansha Singh [aut, cre]

HaploBreedR_0.99.1.tar.gz
HaploBreedR_0.99.1.zip(r-4.7-any)HaploBreedR_0.99.1.zip(r-4.6-any)HaploBreedR_0.99.1.zip(r-4.5-any)
HaploBreedR_0.99.1.tgz(r-4.6-any)HaploBreedR_0.99.1.tgz(r-4.5-any)
HaploBreedR_0.99.1.tar.gz(r-4.7-any)HaploBreedR_0.99.1.tar.gz(r-4.6-any)
HaploBreedR_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HaploBreedR/json (API)

# Install 'HaploBreedR' in R:

install.packages('HaploBreedR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aksruchi/haplobreedr/issues

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

On CRAN:

software genetics genomewideassociation snp genomeassembly network principalcomponent networkenrichment go functionalgenomics functionalprediction geneprediction

3.00 score 33 exports 59 dependencies

Last updated from:f2e6d24e46. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	169
linux-devel	OK	157
source / vignettes	OK	296
linux-release	OK	159
macos-release	OK	148
macos-oldrel	OK	118
windows-devel	OK	145
windows-release	OK	186
windows-oldrel	OK	90
wasm-release	OK	144

Exports:haplobreed_analysis hbr_advanced_decision hbr_annotate_regions_with_genes hbr_build_grm hbr_build_manuscript_tables hbr_check_inputs hbr_crop_lookup hbr_cross_design hbr_cross_plan hbr_cross_usefulness hbr_fit_models hbr_gene_carriers hbr_generate_input_qc_report hbr_go_enrichment hbr_haplotype_block_table hbr_haplotype_blocks hbr_palette hbr_palette_names hbr_plot_cross_ranking hbr_plot_cv_forest hbr_plot_gene_structure hbr_plot_haplotype hbr_plot_haplotype_network hbr_population_size hbr_pyramid_probability hbr_read_gff3_genes hbr_read_results hbr_regate hbr_reml_two_kernel hbr_rice_genetic_map hbr_theme hbr_theme_names hbr_trait_conflicts

Dependencies:askpass BEDMatrix BH BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops boot cigarillo cli codetools cpp11 crayon crochet curl data.table farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite labeling lambda.r lifecycle mime openssl R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Vectors S7 scales Seqinfo snow sys vctrs viridisLite withr XML XVector yaml

HaploBreedR: haplotype-based breeding decisions

Rendered fromHaploBreedR.Rmdusingknitr::rmarkdown

Last update: 2026-10-04
Started: 2026-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Single-trait identification of genes carrying superior haplotypes	haplobreed_analysis
Breeding decisions from HaploBreedR output	hbr_advanced_decision
Annotate LD regions with genes	hbr_annotate_regions_with_genes
Streamed Genomic Relationship Matrix	hbr_build_grm
Build a manuscript-ready multi-sheet Excel workbook from a pipeline run	hbr_build_manuscript_tables
Pre-flight Validation of Inputs	hbr_check_inputs
Common crops mapped to their Ensembl Plants species and assembly	hbr_crop_lookup
Design crosses from a fitted model	hbr_cross_design
Plan a cross between named parents	hbr_cross_plan
Analytical Cross Usefulness	hbr_cross_usefulness
Fit genomic prediction models and rank parents	hbr_fit_models
Carrier status of the superior haplotype at a gene	hbr_gene_carriers
Generate a unified input-QC report	hbr_generate_input_qc_report
GO term enrichment across a set of genes	hbr_go_enrichment
Haplotype block table from a set of target loci	hbr_haplotype_block_table
Haplotype blocks of target loci	hbr_haplotype_blocks
Return `n` colours from a named palette	hbr_palette
Names of the built-in colour palettes	hbr_palette_names
Plot cross ranking by usefulness vs mid-parent index	hbr_plot_cross_ranking
Forest plot of cross-validation comparisons	hbr_plot_cv_forest
Plot gene structure for one or more genes	hbr_plot_gene_structure
Plot haplotype boxplot with summary table	hbr_plot_haplotype
Plot a haplotype network for one or more genes	hbr_plot_haplotype_network
Population Size for Recombinant Recovery	hbr_population_size
Haplotype Pyramiding Probability	hbr_pyramid_probability
Parse gene features from a GFF3 into a data.table	hbr_read_gff3_genes
Read finished HaploBreedR results from disk or memory	hbr_read_results
Re-apply the superior-haplotype rule with different settings	hbr_regate
Spectral Two-Kernel REML	hbr_reml_two_kernel
Bundled rice genetic map anchors	hbr_rice_genetic_map
Return a named HaploBreedR ggplot2 theme	hbr_theme
Names of the built-in ggplot2 themes	hbr_theme_names
Multi-Trait Haplotype Breeding Conflicts	hbr_trait_conflicts
Plot an hbr_run object	plot.hbr_run
Plot an hgsi_advanced object	plot.hgsi_advanced
Print an `hbr_blocks` result	print.hbr_blocks
Print a genotype-reference compatibility report	print.hbr_compat_report
Print an hbr_genotype object	print.hbr_genotype
Print an individual-ID match report	print.hbr_id_report
Print an hbr_reference object	print.hbr_reference
Print an `hbr_regate` result	print.hbr_regate
Print an hbr_run object	print.hbr_run
Print a sequence-resource QC report	print.hbr_sequence_qc
Print an hgsi_advanced object	print.hgsi_advanced
Print an hgsi_fit object	print.hgsi_fit
Summary of an hbr_run object	summary.hbr_run
Summarise an hgsi_advanced object	summary.hgsi_advanced
Summarise an hgsi_fit object	summary.hgsi_fit