BOBaFIT
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BOBaFIT.
Refitting diploid region profiles using a clustering procedure
Bioconductor version: 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("BOBaFIT")):
Installation
To install this package, start R (version "4.2") 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 | 1.2.0 |
| 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 | |
| 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_1.2.0.tar.gz |
| Windows Binary | BOBaFIT_1.2.0.zip |
| macOS Binary (x86_64) | BOBaFIT_1.2.0.tgz |
| macOS Binary (arm64) | BOBaFIT_1.2.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |