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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

To view documentation for the version of this package installed in your system, start R and enter:

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

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
See More
Suggests rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat
Linking To
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BOBaFIT_1.7.0.tar.gz
Windows Binary BOBaFIT_1.7.0.zip
macOS Binary (x86_64) BOBaFIT_1.7.0.tgz
macOS Binary (arm64) BOBaFIT_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BOBaFIT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BOBaFIT
Bioc Package Browser https://code.bioconductor.org/browse/BOBaFIT/
Package Short Url https://bioconductor.org/packages/BOBaFIT/
Package Downloads Report Download Stats