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Bioconductor - BOBaFIT

BOBaFIT

This is the released version of BOBaFIT; for the devel version, see BOBaFIT.

Refitting diploid region profiles using a clustering procedure

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews Clustering, CopyNumberVariation, Normalization, Software, Visualization Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 Package Archives

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

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