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MinimumDistance

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

Bioconductor version: Release (3.17)

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 "4.3") 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")
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 1.44.0
In Bioconductor since BioC 2.10 (R-2.15) (11.5 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
Linking To
Suggests human610quadv1bCrlmm(>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit
System Requirements
Enhances snow, doSNOW
URL
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Package Archives

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

Source Package MinimumDistance_1.44.0.tar.gz
Windows Binary MinimumDistance_1.44.0.zip (64-bit only)
macOS Binary (x86_64) MinimumDistance_1.44.0.tgz
macOS Binary (arm64) MinimumDistance_1.44.0.tgz
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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