Package: IdeoViz 1.43.0
Shraddha Pai
IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram
Plots data associated with arbitrary genomic intervals along chromosomal ideogram.
Authors:
IdeoViz_1.43.0.tar.gz
IdeoViz_1.43.0.zip(r-4.5)IdeoViz_1.43.0.zip(r-4.4)IdeoViz_1.43.0.zip(r-4.3)
IdeoViz_1.43.0.tgz(r-4.4-any)IdeoViz_1.43.0.tgz(r-4.3-any)
IdeoViz_1.43.0.tar.gz(r-4.5-noble)IdeoViz_1.43.0.tar.gz(r-4.4-noble)
IdeoViz_1.43.0.tgz(r-4.4-emscripten)IdeoViz_1.43.0.tgz(r-4.3-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-1.41.0(bioc 3.20)IdeoViz-1.40.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 26 days agofrom:b8543cd58d. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:avgByBingetBinsgetIdeoplotChromValuePairplotOnIdeo
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc
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 |
