CRAN/E | DiNAMIC.Duo

DiNAMIC.Duo

Finding Recurrent DNA Copy Number Alterations and Differences

Installation

About

In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) doi:10.1093/bioinformatics/btq717 and leverages the theory developed in Walter et al. (2015) doi:10.1093/biomet/asv046. An article describing DiNAMIC.Duo by Walter et al. (2022) can be found at doi:10.1093/bioinformatics/btac542.

System requirements Python, NumPy Python library

Key Metrics

Version 1.0.2
R ≥ 3.5.0
Published 2023-03-02 414 days ago
Needs compilation? no
License GPL-3
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Maintainer

Maintainer

Vonn Walter

vwalter1@pennstatehealth.psu.edu

Authors

Vonn Walter

aut / cre

Hyo Young Choi

aut

Xiaobei Zhao

aut

Yan Gao

aut

David Neil Hayes

aut

Material

README
NEWS
Reference manual
Package source

Vignettes

DiNAMICDuo vignette

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

DiNAMIC.Duo archive

Depends

R ≥ 3.5.0

Imports

biomaRt
dinamic
plyr

Suggests

R.rsp