MinimumDistance

DOI: 10.18129/B9.bioc.MinimumDistance    

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

Bioconductor version: Release (3.15)

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>

Installation

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

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

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")

 

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

Details

biocViews	CopyNumberVariation, Microarray, SNP, Software
Version	1.40.0
In Bioconductor since	BioC 2.10 (R-2.15) (10.5 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
LinkingTo
Suggests	human610quadv1bCrlmm(>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit
SystemRequirements
Enhances	snow, doSNOW
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	MinimumDistance_1.40.0.tar.gz
Windows Binary	MinimumDistance_1.40.0.zip (64-bit only)
macOS Binary (x86_64)	MinimumDistance_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MinimumDistance
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MinimumDistance
Package Short Url	https://bioconductor.org/packages/MinimumDistance/
Package Downloads Report	Download Stats