comapr

DOI: 10.18129/B9.bioc.comapr    

Crossover analysis and genetic map construction

Bioconductor version: Release (3.16)

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 "4.2") 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 1.2.0
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_1.2.0.tar.gz
Windows Binary comapr_1.2.0.zip
macOS Binary (x86_64) comapr_1.2.0.tgz
macOS Binary (arm64) comapr_1.2.0.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

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