BOBaFIT
Refitting diploid region profiles using a clustering procedure
Bioconductor version: Release (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("BOBaFIT")
):
Installation
To install this package, start R (version "4.4") 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 |
Details
biocViews | Clustering, CopyNumberVariation, Normalization, Software, Visualization |
Version | 1.8.0 |
In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
See More
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 | BOBaFIT_1.8.0.tar.gz |
Windows Binary | BOBaFIT_1.8.0.zip (64-bit only) |
macOS Binary (x86_64) | BOBaFIT_1.8.0.tgz |
macOS Binary (arm64) | BOBaFIT_1.8.0.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 |