BOBaFIT

DOI: 10.18129/B9.bioc.BOBaFIT    

Refitting diploid region profiles using a clustering procedure

Bioconductor version: Release (3.15)

This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

Author: Andrea Poletti [aut], Gaia Mazzocchetti [aut, cre], Vincenza Solli [aut]

Maintainer: Gaia Mazzocchetti <bioinformatic.seragnoli at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("BOBaFIT")

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("BOBaFIT")

 

HTML	R Script	BOBaFIT.Rmd
HTML	R Script	Data preparation using TCGA-BRCA database.Rmd
PDF		Reference Manual

Details

biocViews	Clustering, CopyNumberVariation, Normalization, Software, Visualization
Version	1.0.1
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL (>= 3)
Depends	R (>= 2.10)
Imports	dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr
LinkingTo
Suggests	rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat
SystemRequirements
Enhances
URL	https://github.com/andrea-poletti-unibo/BOBaFIT
BugReports	https://github.com/andrea-poletti-unibo/BOBaFIT/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	BOBaFIT_1.0.1.tar.gz
Windows Binary	BOBaFIT_1.0.1.zip
macOS Binary (x86_64)	BOBaFIT_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BOBaFIT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BOBaFIT
Package Short Url	https://bioconductor.org/packages/BOBaFIT/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive