BOBaFIT

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

Refitting diploid region profiles using a clustering procedure

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DOI: 10.18129/B9.bioc.BOBaFIT

Bioconductor version: Release (3.22)

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")

BOBaFIT.Rmd HTML R Script

Data preparation using TCGA-BRCA database.Rmd HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, CopyNumberVariation, Normalization, Software, Visualization

Version 1.14.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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

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Package Archives

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

Source Package BOBaFIT_1.14.0.tar.gz

Windows Binary (x86_64) BOBaFIT_1.14.0.zip (64-bit only)

macOS Binary (x86_64) BOBaFIT_1.14.0.tgz

macOS Binary (arm64) BOBaFIT_1.14.0.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/

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