comapr

This is the released version of comapr; for the devel version, see comapr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Crossover analysis and genetic map construction

Bioconductor version: Release (3.23)

comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.

Author: Ruqian Lyu [aut, cre] ORCID: 0000-0002-7736-6612

Maintainer: Ruqian Lyu <xiaoru.best at gmail.com>

Citation (from within R, enter citation("comapr")):

Ruqian Lyu. comapr: Crossover analysis and genetic map construction. doi:10.18129/B9.bioc.comapr, R package version 1.16.0, https://bioconductor.org/packages/comapr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("comapr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("comapr")

Get-Started-With-comapr	HTML	R Script
single-sperm-co-analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Genetics, SingleCell, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	comapr_1.16.0.tar.gz
Windows Binary (x86_64)	comapr_1.16.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	comapr_1.16.0.tgz
macOS Binary (sonoma-arm64)	comapr_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/comapr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/comapr
Package Short Url	https://bioconductor.org/packages/comapr/
Package Downloads Report	Download Stats