Package: IdeoViz 1.47.0
Shraddha Pai
IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram
Plots data associated with arbitrary genomic intervals along chromosomal ideogram.
Authors:
IdeoViz_1.47.0.tar.gz
IdeoViz_1.47.0.zip(r-4.6)IdeoViz_1.47.0.zip(r-4.5)
IdeoViz_1.47.0.tgz(r-4.6-any)IdeoViz_1.47.0.tgz(r-4.5-any)
IdeoViz_1.47.0.tar.gz(r-4.6-any)IdeoViz_1.47.0.tar.gz(r-4.5-any)
IdeoViz_1.47.0.tgz(r-4.5-emscripten)
IdeoViz.pdf |IdeoViz.html✨
IdeoViz/json (API)
NEWS
| # Install 'IdeoViz' in R: |
| install.packages('IdeoViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- GSM733664_broadPeaks - Data for vignette example 4.
- binned_fullGenome - Data for example 3.
- binned_multiSeries - Data for vignette example 1.
- binned_singleSeries - Data for example 2.
- hg18_ideo - Ideogram table for hg18
- wins - Data for vignette example 1.
- wins - Data for vignette example 1.
- wins_discrete - Data for example 2.
- wins_discrete - Data for example 2.
- wins_entiregenome - Data for example 3.
- wins_entiregenome - Data for example 3.
On BioConductor:IdeoViz-1.47.0(bioc 3.23)IdeoViz-1.46.0(bioc 3.22)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:847e77cbd3. Checks:1 ERROR, 6 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 180 | ||
| linux-devel-x86_64 | WARNING | 248 | ||
| source / vignettes | OK | 203 | ||
| linux-release-x86_64 | WARNING | 249 | ||
| macos-devel-arm64 | WARNING | 168 | ||
| macos-release-arm64 | WARNING | 121 | ||
| windows-devel | WARNING | 169 | ||
| windows-release | WARNING | 168 | ||
| wasm-release | OK | 147 |
Exports:avgByBingetBinsgetIdeoplotChromValuePairplotOnIdeo
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plots continuous or discrete data along chromosomal ideogram | IdeoViz-package |
| Aggregates data by genomic bins | avgByBin |
| Data for example 3. | binned_fullGenome |
| Data for vignette example 1. | binned_multiSeries |
| Data for example 2. | binned_singleSeries |
| getBins | getBins |
| Download ideogram table from UCSC | getIdeo |
| Data for vignette example 4. | GSM733664_broadPeaks |
| Ideogram table for hg18 | hg18_ideo |
| Base function which plots the ideogram and superimposed data for a single chromosome. plotOnIdeo() calls this function and stacks the resulting output. | plotChromValuePair |
| Plot data superimposed on chromosomal ideogram | plotOnIdeo |
| Data for vignette example 1. | wins |
| Data for example 2. | wins_discrete |
| Data for example 3. | wins_entiregenome |
