comapr

DOI: 10.18129/B9.bioc.comapr    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see comapr.

Crossover analysis and genetic map construction

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Genetics, SingleCell, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	comapr_1.0.0.tar.gz
Windows Binary	comapr_1.0.0.zip
macOS Binary (x86_64)	comapr_1.0.0.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