BOBaFIT

DOI: 10.18129/B9.bioc.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 (3.16)

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 "4.2") 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")

 

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 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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_1.1.0.tar.gz
Windows Binary BOBaFIT_1.1.0.zip
macOS 10.13 (High Sierra) BOBaFIT_1.1.0.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

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