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comapr

This is the development version of comapr; for the stable release version, see comapr.

Crossover analysis and genetic map construction


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Genetics, SingleCell, Software, Visualization
Version 1.7.1
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
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Package Archives

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

Source Package comapr_1.7.1.tar.gz
Windows Binary
macOS Binary (x86_64) comapr_1.7.1.tgz
macOS Binary (arm64)
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