Package: RiboCrypt 1.19.0
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_1.19.0.tar.gz
RiboCrypt_1.19.0.zip(r-4.7)RiboCrypt_1.19.0.zip(r-4.6)RiboCrypt_1.19.0.zip(r-4.5)
RiboCrypt_1.19.0.tgz(r-4.6-any)RiboCrypt_1.19.0.tgz(r-4.5-any)
RiboCrypt_1.19.0.tar.gz(r-4.7-any)RiboCrypt_1.19.0.tar.gz(r-4.6-any)
RiboCrypt_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.19.0(bioc 3.24)RiboCrypt-1.18.0(bioc 3.23)
softwaresequencingriboseqrnaseq
Last updated from:cbd1ebc4a0. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 305 | ||
| linux-devel-x86_64 | NOTE | 565 | ||
| source / vignettes | OK | 483 | ||
| linux-release-x86_64 | NOTE | 564 | ||
| macos-release-arm64 | NOTE | 337 | ||
| macos-oldrel-arm64 | NOTE | 385 | ||
| windows-devel | NOTE | 450 | ||
| windows-release | NOTE | 457 | ||
| windows-oldrel | NOTE | 431 | ||
| wasm-release | OK | 260 |
Exports:browseRCcollection_dir_from_expcollection_path_from_expDEG_plotmake_rc_urlmultiOmicsPlot_animatemultiOmicsPlot_listmultiOmicsPlot_ORFikExpRiboCrypt_app
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtbiomartrBiostringsbitbit64bitopsblobBSgenomebslibcachemcigarillocirclizeclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDESeq2digestdoParalleldownloaderdplyrDTevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelitedownlocfitmagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimeNGLVieweRopensslORFikotelphilentropypillarpkgconfigplotlypngpoormanprettyunitsprogresspromisespurrrqs2R.methodsS3R.ooR.utilsR6rappdirsrclipboardRColorBrewerRcppRcppArmadilloRcppParallelRCurlreadrrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinycssloadersshinyhelpershinyjquishinyjsshinyWidgetssnowsourcetoolsSparseArraystringfishstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.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 |