Package: BOBaFIT 1.17.0

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_1.17.0.tar.gz
BOBaFIT_1.17.0.zip(r-4.7)BOBaFIT_1.17.0.zip(r-4.6)BOBaFIT_1.17.0.zip(r-4.5)
BOBaFIT_1.17.0.tgz(r-4.6-any)BOBaFIT_1.17.0.tgz(r-4.5-any)
BOBaFIT_1.17.0.tar.gz(r-4.7-any)BOBaFIT_1.17.0.tar.gz(r-4.6-any)
BOBaFIT_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BOBaFIT/json (API)

# Install 'BOBaFIT' in R:
install.packages('BOBaFIT', repos = c('https://bioc.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 6 exports 141 dependencies

Last updated from:267dba8135. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING238
linux-devel-x86_64WARNING501
source / vignettesOK362
linux-release-x86_64WARNING455
macos-release-arm64WARNING271
macos-oldrel-arm64WARNING281
windows-develWARNING430
windows-releaseWARNING409
windows-oldrelWARNING429
wasm-releaseOK207

Exports:%>%computeNormalChromosomesDRrefitDRrefit_plotPlotChrClusterPopeye

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggforceggplot2gluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeNbClustnnetopensslOrganismDbipillarpkgconfigplyrplyrangespngpolyclipProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextweenrUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

BOBaFIT
Introduction | Data | BOBaFIT Workflow | ComputeNormalChromosome | DRrefit | The Dataframes | DRrefit_plot | PlotChrCluster | Session info | Reference
Rendered fromBOBaFIT.Rmdusingknitr::rmarkdown

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

Data preparation using TCGA-BRCA database
Introduction | Download from TCGA | Columns preparation | Assign the chromosome arm with Popeye | Calculation of the Copy Number | Session info
Rendered fromData-Preparation.Rmdusingknitr::rmarkdown

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