Package: rGenomeTracks 1.13.0
Omar Elashkar
rGenomeTracks: Integerated visualization of epigenomic data
rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.
Authors:
rGenomeTracks_1.13.0.tar.gz
rGenomeTracks_1.13.0.zip(r-4.5)rGenomeTracks_1.13.0.zip(r-4.4)rGenomeTracks_1.13.0.zip(r-4.3)
rGenomeTracks_1.13.0.tgz(r-4.4-any)rGenomeTracks_1.13.0.tgz(r-4.3-any)
rGenomeTracks_1.13.0.tar.gz(r-4.5-noble)rGenomeTracks_1.13.0.tar.gz(r-4.4-noble)
rGenomeTracks_1.13.0.tgz(r-4.4-emscripten)rGenomeTracks_1.13.0.tgz(r-4.3-emscripten)
rGenomeTracks.pdf |rGenomeTracks.html✨
rGenomeTracks/json (API)
| # Install 'rGenomeTracks' in R: |
| install.packages('rGenomeTracks', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:rGenomeTracks-1.13.0(bioc 3.21)rGenomeTracks-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:c6e4fb57bb. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:epilogos_jsoninstall_pyGenomeTracksplot_gtrackstrack_bedtrack_bedgraphtrack_bedgraph_matrixtrack_bigwigtrack_domainstrack_epilogostrack_gtftrack_hic_matrixtrack_hlinestrack_linkstrack_narrow_peaktrack_scalebartrack_spacertrack_vlinestrack_x_axis
Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbmpcachemclicpp11crayoncurlDBIdbplyrdigestdownloaderdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataglueherehttrigraphimagerIRangesjpegjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcppRcppTOMLreadbitmapreticulaterGenomeTracksDatarlangrprojrootRSQLiteS4VectorsstringistringrsystibbletidyrtidyselecttiffUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adding genome_track Objects | +,genome_track,genome_track-method |
| Generate epilogo json configuration file | epilogos_json |
| Install pyGenomeTracks Dependency | install_pyGenomeTracks |
| Plotting genomic tracks | genome_track plot_gtracks plot_gtracks, plot_gtracks,genome_track-method |
| Generate bed track | track_bed |
| Generate bedgraph track | track_bedgraph |
| Generate bedgraph matrix track | track_bedgraph_matrix |
| Generate bigwig track | track_bigwig |
| Generate domains track | track_domains |
| Generate epilogos track | track_epilogos |
| Generate gtf track | track_gtf |
| Generate HiC track | track_hic_matrix |
| Generate a track with horizontal lines | track_hlines |
| Generate links track | track_links |
| Generate narrow peaks track | track_narrow_peak |
| Generate scalebar track | track_scalebar |
| Generate spacing track | track_spacer |
| Overlay vertical lines from a bed file | track_vlines |
| Specify x_axis option for genome_track. | track_x_axis |