CNVgears

DOI: 10.18129/B9.bioc.CNVgears    

A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results

Bioconductor version: Release (3.13)

This package contains a set of functions to perform several type of processing and analysis on CNVs calling pipelines/algorithms results in an integrated manner and regardless of the raw data type (SNPs array or NGS). It provides functions to combine multiple CNV calling results into a single object, filter them, compute CNVRs (CNV Regions) and inheritance patterns, detect genic load, and more. The package is best suited for studies in human family-based cohorts.

Author: Simone Montalbano [cre, aut]

Maintainer: Simone Montalbano <simone.montalbano at protonmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("CNVgears")

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("CNVgears")

 

HTML	R Script	CNVgears package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Preprocessing, Software, WorkflowStep
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	GPL-3
Depends	R (>= 4.1), data.table
Imports	ggplot2
LinkingTo
Suggests	VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR, rmarkdown, devtools, cowplot, usethis, scales, testthat, GenomicRanges, cn.mops, R.utils
SystemRequirements
Enhances
URL
BugReports	https://github.com/SinomeM/CNVgears/issues
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	CNVgears_1.0.0.tar.gz
Windows Binary	CNVgears_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CNVgears_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNVgears
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVgears
Package Short Url	https://bioconductor.org/packages/CNVgears/
Package Downloads Report	Download Stats