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 (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | BOBaFIT_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | BOBaFIT_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | BOBaFIT_1.16.0.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 |