Package: rGenomeTracks 1.19.0
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_1.19.0.tar.gz
rGenomeTracks_1.19.0.zip(r-4.7)rGenomeTracks_1.19.0.zip(r-4.6)rGenomeTracks_1.19.0.zip(r-4.5)
rGenomeTracks_1.19.0.tgz(r-4.6-any)rGenomeTracks_1.19.0.tgz(r-4.5-any)
rGenomeTracks_1.19.0.tar.gz(r-4.7-any)rGenomeTracks_1.19.0.tar.gz(r-4.6-any)
rGenomeTracks_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.19.0(bioc 3.24)rGenomeTracks-1.18.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:8fe422af4e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 159 | ||
| linux-devel-x86_64 | NOTE | 208 | ||
| source / vignettes | OK | 212 | ||
| linux-release-x86_64 | NOTE | 227 | ||
| macos-release-arm64 | NOTE | 131 | ||
| macos-oldrel-arm64 | NOTE | 127 | ||
| windows-devel | NOTE | 360 | ||
| windows-release | NOTE | 454 | ||
| windows-oldrel | NOTE | 417 | ||
| wasm-release | OK | 133 |
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:AnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbmpcachemclicpp11crayoncurlDBIdbplyrdigestdownloaderdplyrfastmapfilelockgenericsglueherehttrhttr2igraphimagerIRangesjpegjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcppRcppTOMLreadbitmapreticulaterGenomeTracksDatarlangrprojrootRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselecttiffutf8vctrswithrXVectoryaml
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 |