Package: biovizBase 1.55.0
Michael Lawrence
biovizBase: Basic graphic utilities for visualization of genomic data.
The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
Authors:
biovizBase_1.55.0.tar.gz
biovizBase_1.55.0.zip(r-4.5)biovizBase_1.55.0.zip(r-4.4)biovizBase_1.55.0.zip(r-4.3)
biovizBase_1.55.0.tgz(r-4.4-x86_64)biovizBase_1.55.0.tgz(r-4.4-arm64)biovizBase_1.55.0.tgz(r-4.3-x86_64)biovizBase_1.55.0.tgz(r-4.3-arm64)
biovizBase_1.55.0.tar.gz(r-4.5-noble)biovizBase_1.55.0.tar.gz(r-4.4-noble)
biovizBase_1.55.0.tgz(r-4.4-emscripten)biovizBase_1.55.0.tgz(r-4.3-emscripten)
biovizBase.pdf |biovizBase.html✨
biovizBase/json (API)
NEWS
| # Install 'biovizBase' in R: |
| install.packages('biovizBase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- crc.gr - CRC
- crc1.GeRL - Crc1.GeRL
- darned_hg19_subset500 - Subset of RNA editing sites in hg19...
- genesymbol - Gene symbols with position...
- hg19Ideogram - Hg19 ideogram without cytoband information...
- hg19IdeogramCyto - Hg19 ideogram with cytoband information...
- hg19sub - CRC
- ideo - Ideogram without cytoband information
- ideoCyto - Ideogram with cytoband information
- mut.gr - CRC
On BioConductor:biovizBase-1.55.0(bioc 3.21)biovizBase-1.54.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
infrastructurevisualizationpreprocessing
Last updated 2 months agofrom:85d7c9482f. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 19 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 19 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 19 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 19 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 19 2024 |
Exports:addSteppingblind.pal.infobrewer.pal.blind.infocolorBlindSafePalcontainLetterscrunchdichromat.pal.blind.infoestimateCoverageflatGrlGCcontentgenBlindPalInfogenBrewerBlindPalInfogenDichromatPalInfogetBioColorgetFormalNamesgetGapsgetIdeoGRgetIdeogramgetScalegetXLabgetXScalegetYLabis_coord_genomeis_coord_truncate_gapsisIdeogramisJunctionReadisMatchedWithModelisSimpleIdeogrammaxGapmoldparseArgsForAesparseArgsForNonAespileupAsGRangespileupGRangesAsVariantTableplotColorLegendshowColorshrinkageFunsplitByFacetsstrip_formula_dotssubsetArgsByFormalstransformDfToGrtransformGRangesForEvenSpacetransformToBarInCircletransformToCircletransformToDftransformToGenometransformToLinkInCircletransformToRectInCircletransformToSegInCircle
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericsR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| biovizBase is a package which provides utilities and color scheme... | biovizBase-package biovizBase |
| Adding disjoint levels to a GenomicRanges object | addStepping addStepping,GenomicRanges-method |
| Color blind safe palette generator | blind.pal.info brewer.pal.blind.info colorBlindSafePal dichromat.pal.blind.info genBlindPalInfo genBrewerBlindPalInfo genDichromatPalInfo |
| Checking if string contains letters or not | containLetters |
| CRC | CRC crc.gr hg19sub mut.gr |
| crc1.GeRL | crc1.GeRL |
| Fetching GRanges from various data source | crunch crunch,BamFile-method crunch,EnsDb-method crunch,GAlignments-method crunch,TxDb-method |
| Subset of RNA editing sites in hg19... | darned_hg19_subset500 |
| Estimation of Coverage | estimateCoverage estimateCoverage,BamFile-method |
| Transform GRangesList to GRanges | flatGrl |
| GC content computation for BSgenome | GCcontent |
| Gene symbols with position... | genesymbol |
| Color scheme getter for biological data | getBioColor |
| Get formals from functions | getFormalNames |
| get gaps for a stepping transformed GRanges object | getGaps getGaps,GRanges-method |
| Get ideogram information | getIdeoGR |
| Get ideogram. | getIdeogram |
| Get scale information from a GRanges | getScale |
| get x scale breaks and labels | getXScale getXScale,GRanges-method |
| parse x and y label information from a specific object | getXLab getXLab,GAlignments-method getXLab,GRanges-method getXLab,GRangesList-method getXLab-method getYLab getYLab,TxDb-method |
| Hg19 ideogram without cytoband information... | hg19Ideogram |
| Hg19 ideogram with cytoband information... | hg19IdeogramCyto |
| ideogram without cytoband information | ideo |
| ideogram with cytoband information | ideoCyto |
| Ideogram checking | isIdeogram |
| Utils for Splicing Summary | isJunctionRead isMatchedWithModel |
| Simple ideogram checking | isSimpleIdeogram |
| Estimated max gaps | maxGap maxGap,GenomicRanges-method |
| mold data into data.frame | mold mold,eSet-method mold,ExpressionSet-method mold,GRanges-method mold,GRangesList-method mold,IRanges-method mold,matrix-method mold,RangedSummarizedExperiment-method mold,Rle-method mold,RleList-method mold,Seqinfo-method mold,SummarizedExperiment-method mold,Views-method mold,VRanges-method |
| Utils for parsing (un)evaluated arguments | parseArgsForAes parseArgsForNonAes |
| Summarize reads for certain region | pileupAsGRanges |
| Mismatch summary | pileupGRangesAsVariantTable |
| Show colors | plotColorLegend |
| Show colors | showColor |
| Shrinkage function | is_coord_truncate_gaps shrinkageFun shrinkageFun,GenomicRanges-method shrinkageFun,IRanges-method |
| split a GRanges by formula | splitByFacets splitByFacets,GRanges,formula-method splitByFacets,GRanges,GRanges-method splitByFacets,GRanges,missing-method splitByFacets,GRanges,NULL-method |
| strip dots around a formula variables | strip_formula_dots |
| Subset list of arguments by functions | subsetArgsByFormals |
| Transform GRanges with New Coordinates | transformGRangesForEvenSpace |
| Transform GRanges to different coordinates and layout | is_coord_genome transformDfToGr transformToArch transformToArch,GRanges-method transformToBarInCircle transformToCircle transformToDf transformToDf,GRanges-method transformToDf-method transformToGenome transformToGenome,GRanges-method transformToGenome,GRangesList-method transformToLinkInCircle transformToRectInCircle transformToSegInCircle |
