Package: RiboCrypt 1.13.0

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:Michal Swirski [aut, cre, cph], Haakon Tjeldnes [aut, ctb], Kornel Labun [ctb]

RiboCrypt_1.13.0.tar.gz
RiboCrypt_1.13.0.zip(r-4.5)RiboCrypt_1.13.0.zip(r-4.4)RiboCrypt_1.13.0.zip(r-4.3)
RiboCrypt_1.13.0.tgz(r-4.4-any)RiboCrypt_1.13.0.tgz(r-4.3-any)
RiboCrypt_1.13.0.tar.gz(r-4.5-noble)RiboCrypt_1.13.0.tar.gz(r-4.4-noble)
RiboCrypt_1.13.0.tgz(r-4.4-emscripten)RiboCrypt_1.13.0.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)

software sequencing riboseq rnaseq

5.98 score 5 stars 19 scripts 158 downloads 5 exports 158 dependencies

Last updated 2 months agofrom:148e0911c4. 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:DEG_plot multiOmicsPlot_animate multiOmicsPlot_list multiOmicsPlot_ORFikExp RiboCrypt_app

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt biomartr Biostrings bit bit64 bitops blob BSgenome bslib cachem cli clipr codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DESeq2 digest downloader dplyr evaluate fansi farver fastmap filelock fontawesome formatR fs fst fstcore futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr hms htmltools htmlwidgets httpuv httr httr2 IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell NGLVieweR nlme openssl ORFik philentropy pillar pkgconfig plogr plotly png poorman prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl readr restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales shiny shinycssloaders shinyhelper shinyjqui snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

RiboCryptOverview

Michal Swirski & Hakon Tjeldnes

Rendered fromRiboCrypt_overview.rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2023-04-04
Started: 2021-10-19

App Tutorial

Michal Swirski & Hakon Tjeldnes

Rendered fromRiboCrypt_app_tutorial.rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2023-01-27
Started: 2023-01-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Differential expression plots (1D or 2D)	DEG_plot
Distance to following range	distanceToFollowing
Fetch Javascript sequence	fetch_JS_seq
Fetch summary of uniprot id	fetch_summary
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
Select box for organism	organism_input_select
Create RiboCrypt app	RiboCrypt_app