Package: BOBaFIT 1.9.0
![](https://r-universe.dev/static/nobody.jpg)
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:
BOBaFIT_1.9.0.tar.gz
BOBaFIT_1.9.0.zip(r-4.5)BOBaFIT_1.9.0.zip(r-4.4)BOBaFIT_1.9.0.zip(r-4.3)
BOBaFIT_1.9.0.tgz(r-4.4-any)BOBaFIT_1.9.0.tgz(r-4.3-any)
BOBaFIT_1.9.0.tar.gz(r-4.5-noble)BOBaFIT_1.9.0.tar.gz(r-4.4-noble)
BOBaFIT_1.9.0.tgz(r-4.4-emscripten)BOBaFIT_1.9.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/andrea-poletti-unibo/bobafit/issues
- TCGA_BRCA_CN_segments - Segments of 100 Breast Cancer samples, downloaded from TCGA-BRCA.
On BioConductor:BOBaFIT-1.9.0(bioc 3.20)BOBaFIT-1.8.0(bioc 3.19)
Last updated 2 months agofrom:0637d46500
Exports:%>%computeNormalChromosomesDRrefitDRrefit_plotPlotChrClusterPopeye
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggforceggplot2ggstatsgluegraphgridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellNbClustnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrplyrangespngpolyclipprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextweenrtxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
computeNormalChromosomes | computeNormalChromosomes |
DRrefit | DRrefit |
DRrefit_plot | DRrefit_plot |
PlotChrCluster | PlotChrCluster |
Popeye | Popeye |
Segments of 100 Breast Cancer samples, downloaded from TCGA-BRCA. | TCGA_BRCA_CN_segments |