comapr

Crossover analysis and genetic map construction

Bioconductor version: Release (3.17)

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]

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

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews	Genetics, SingleCell, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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
Linking To
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
System Requirements
Enhances
URL

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Build Report

Package Archives

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

Source Package	comapr_1.4.0.tar.gz
Windows Binary	comapr_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	comapr_1.4.0.tgz
macOS Binary (arm64)	comapr_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/comapr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/comapr
Bioc Package Browser	https://code.bioconductor.org/browse/comapr/
Package Short Url	https://bioconductor.org/packages/comapr/
Package Downloads Report	Download Stats