Package: BOBaFIT 1.11.0

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_1.11.0.tar.gz
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BOBaFIT.pdf |BOBaFIT.html✨
BOBaFIT/json (API)

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

Peer review:

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

Datasets:

On BioConductor:BOBaFIT-1.9.0(bioc 3.20)BOBaFIT-1.8.0(bioc 3.19)

copynumbervariationclusteringvisualizationnormalizationsoftware

3.90 score 3 scripts 158 downloads 6 exports 160 dependencies

Last updated 23 days agofrom:eb24815903. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:%>%computeNormalChromosomesDRrefitDRrefit_plotPlotChrClusterPopeye

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggforceggplot2ggstatsgluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellNbClustnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrplyrangespngpolyclipprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextweenrtxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

BOBaFIT

Gaia Mazzocchetti

Rendered fromBOBaFIT.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Data preparation using TCGA-BRCA database

Gaia Mazzocchetti

Rendered fromData-Preparation.Rmdusingknitr::rmarkdownon Oct 30 2024.

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