BOBaFIT

This is the development version of BOBaFIT; for the stable release version, see BOBaFIT.

Refitting diploid region profiles using a clustering procedure

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("BOBaFIT")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BOBaFIT")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, CopyNumberVariation, Normalization, Software, Visualization
Version	1.7.0
In Bioconductor since	BioC 3.15 (R-4.2) (2 years)
License	GPL (>= 3)
Depends	R (>= 2.10)
Imports	dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr
System Requirements
URL	https://github.com/andrea-poletti-unibo/BOBaFIT
Bug Reports	https://github.com/andrea-poletti-unibo/BOBaFIT/issues

Suggests	rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat
Linking To
Enhances
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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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