MinimumDistance
This is the released version of MinimumDistance; for the devel version, see MinimumDistance.
A Package for De Novo CNV Detection in Case-Parent Trios
Bioconductor version: Release (3.23)
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("MinimumDistance")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.56.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), VanillaICE(>= 1.47.1) |
| Imports | methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors(>= 0.23.18), IRanges, Seqinfo, 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_1.56.0.tar.gz |
| Windows Binary (x86_64) | MinimumDistance_1.56.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MinimumDistance_1.56.0.tgz |
| macOS Binary (sonoma-arm64) | MinimumDistance_1.56.0.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/ |
| Package Downloads Report | Download Stats |