MinimumDistance
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MinimumDistance.
A Package for De Novo CNV Detection in Case-Parent Trios
Bioconductor version: 3.9
Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
Author: Robert B Scharpf and Ingo Ruczinski
Maintainer: Robert B Scharpf <rscharpf at jhu.edu>
Citation (from within R, enter
citation("MinimumDistance")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Microarray, SNP, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3), VanillaICE(>= 1.31.3) |
| Imports | methods, BiocGenerics, Biobase, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges(>= 1.17.16), SummarizedExperiment(>= 0.2.0), 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, SNPchip, 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_1.28.0.tar.gz |
| Windows Binary | MinimumDistance_1.28.0.zip |
| Mac OS X 10.11 (El Capitan) | MinimumDistance_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MinimumDistance |
| Source Repository (Developer Access) | git clone [email protected]:packages/MinimumDistance |
| Bioc Package Browser | https://code.bioconductor.org/browse/MinimumDistance/ |
| Package Short Url | https://bioconductor.org/packages/MinimumDistance/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |