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MinimumDistance

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

A Package for De Novo CNV Detection in Case-Parent Trios


Bioconductor version: Development (3.19)

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

Author: Robert B Scharpf and Ingo Ruczinski

Maintainer: Robert Scharpf <rscharpf at jhu.edu>

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

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("MinimumDistance")

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("MinimumDistance")
Detection of de novo copy number alterations in case-parent trios PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Microarray, SNP, Software
Version 1.47.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0
Depends R (>= 3.5.0), VanillaICE(>= 1.47.1)
Imports methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors(>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges(>= 1.17.16), SummarizedExperiment(>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils
System Requirements
URL
See More
Suggests human610quadv1bCrlmm(>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit
Linking To
Enhances snow, doSNOW
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MinimumDistance_1.47.0.tar.gz
Windows Binary MinimumDistance_1.47.0.zip
macOS Binary (x86_64) MinimumDistance_1.47.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MinimumDistance
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MinimumDistance
Bioc Package Browser https://code.bioconductor.org/browse/MinimumDistance/
Package Short Url https://bioconductor.org/packages/MinimumDistance/
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