Package: BOBaFIT 1.16.0

Gaia Mazzocchetti

BOBaFIT: Refitting diploid region profiles using a clustering procedure

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.

Authors:Andrea Poletti [aut], Gaia Mazzocchetti [aut, cre], Vincenza Solli [aut]

BOBaFIT_1.16.0.tar.gz
BOBaFIT_1.16.0.zip(r-4.7)BOBaFIT_1.16.0.zip(r-4.6)BOBaFIT_1.16.0.zip(r-4.5)
BOBaFIT_1.16.0.tgz(r-4.6-any)BOBaFIT_1.16.0.tgz(r-4.5-any)
BOBaFIT_1.16.0.tar.gz(r-4.7-any)BOBaFIT_1.16.0.tar.gz(r-4.6-any)
BOBaFIT_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BOBaFIT/json (API)

# Install 'BOBaFIT' in R:
install.packages('BOBaFIT', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/andrea-poletti-unibo/bobafit/issues

Datasets:

On BioConductor:BOBaFIT-1.17.0(bioc 3.24)BOBaFIT-1.16.0(bioc 3.23)

copynumbervariationclusteringvisualizationnormalizationsoftware

3.90 score 4 scripts 320 downloads 6 exports 140 dependencies

Last updated from:6e021a1b29 (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING238
linux-devel-x86_64WARNING522
source / vignettesOK363
linux-release-x86_64WARNING549
macos-release-arm64WARNING365
macos-oldrel-arm64WARNING469
windows-develWARNING443
windows-releaseWARNING418
windows-oldrelWARNING449
wasm-releaseOK177

Exports:%>%computeNormalChromosomesDRrefitDRrefit_plotPlotChrClusterPopeye

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggforceggplot2gluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeNbClustnnetopensslOrganismDbipillarpkgconfigplyrplyrangespngpolyclipProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextweenrUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

BOBaFIT

Gaia Mazzocchetti

Rendered fromBOBaFIT.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2022-05-25
Started: 2021-05-04

Data preparation using TCGA-BRCA database

Gaia Mazzocchetti

Rendered fromData-Preparation.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2022-05-25
Started: 2021-10-20