Package: RiboCrypt 1.13.2
Michal Swirski
RiboCrypt: Interactive visualization in genomics
R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.
Authors:
RiboCrypt_1.13.2.tar.gz
RiboCrypt_1.13.2.zip(r-4.5)RiboCrypt_1.13.2.zip(r-4.4)RiboCrypt_1.13.2.zip(r-4.3)
RiboCrypt_1.13.2.tgz(r-4.5-any)RiboCrypt_1.13.2.tgz(r-4.4-any)RiboCrypt_1.13.2.tgz(r-4.3-any)
RiboCrypt_1.13.2.tar.gz(r-4.5-noble)RiboCrypt_1.13.2.tar.gz(r-4.4-noble)
RiboCrypt_1.13.2.tgz(r-4.4-emscripten)RiboCrypt_1.13.2.tgz(r-4.3-emscripten)
RiboCrypt.pdf |RiboCrypt.html✨
RiboCrypt/json (API)
| # Install 'RiboCrypt' in R: |
| install.packages('RiboCrypt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/m-swirski/ribocrypt/issues
On BioConductor:RiboCrypt-1.13.0(bioc 3.21)RiboCrypt-1.12.0(bioc 3.20)
softwaresequencingriboseqrnaseq
Last updated 1 days agofrom:baae084618. Checks:1 OK, 8 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 29 2025 |
| R-4.5-win | ERROR | Mar 29 2025 |
| R-4.5-mac | ERROR | Mar 29 2025 |
| R-4.5-linux | ERROR | Mar 29 2025 |
| R-4.4-win | ERROR | Mar 29 2025 |
| R-4.4-mac | ERROR | Mar 29 2025 |
| R-4.4-linux | ERROR | Mar 29 2025 |
| R-4.3-win | ERROR | Mar 29 2025 |
| R-4.3-mac | ERROR | Mar 29 2025 |
Exports:browseRCcollection_dir_from_expcollection_path_from_expDEG_plotmake_rc_urlmultiOmicsPlot_animatemultiOmicsPlot_listmultiOmicsPlot_ORFikExpRiboCrypt_app
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtbiomartrBiostringsbitbit64bitopsblobBSgenomebslibcachemcirclizeclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDESeq2digestdoParalleldownloaderdplyrDTevaluatefansifarverfastmapfilelockfontawesomeforeachformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelitedownlocfitmagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellNGLVieweRnlmeopensslORFikphilentropypillarpkgconfigplogrplotlypngpoormanprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsrclipboardRColorBrewerRcppRcppArmadilloRCurlreadrrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesshapeshinyshinycssloadersshinyhelpershinyjquishinyjssnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8vctrsviridisLitevroomwithrwritexlxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Browse a gene on Ribocrypt webpage | browseRC |
| Get collection directory | collection_dir_from_exp |
| Get collection path | collection_path_from_exp |
| Cast a collection table to wide format | collection_to_wide |
| Get collection table normalized in wide format | compute_collection_table |
| Differential expression plots (1D or 2D) | DEG_plot |
| Fetch Javascript sequence | fetch_JS_seq |
| Fetch summary of uniprot id | fetch_summary |
| Full plot for allsamples browser | get_meta_browser_plot_full |
| Load a ORFik collection table | load_collection |
| Create URL to browse a gene on Ribocrypt webpage | make_rc_url |
| Multi-omics animation using list input | multiOmicsPlot_animate |
| Multi-omics plot using list input | multiOmicsPlot_list |
| Multi-omics plot using ORFik experiment input | multiOmicsPlot_ORFikExp |
| Normalize collection table | normalize_collection |
| Select box for organism | organism_input_select |
| Create RiboCrypt app | RiboCrypt_app |