RiboCrypt

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see RiboCrypt.

Interactive visualization in genomics

Bioconductor version: 3.18

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.

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

Maintainer: Michal Swirski <michal.swirski at uw.edu.pl>

Citation (from within R, enter citation("RiboCrypt")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("RiboCrypt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RiboCrypt")

RiboCrypt_app_tutorial.html HTML R Script

RiboCrypt_overview.html HTML R Script

Reference Manual PDF

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews RNASeq, RiboSeq, Sequencing, Software

Version 1.8.0

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License MIT + file LICENSE

Depends R (>= 3.6.0), ORFik(>= 1.13.12)

Imports bslib, BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, RCurl, shiny, shinycssloaders, shinyhelper, shinyjqui, stringr

System Requirements

URL https://github.com/m-swirski/RiboCrypt

Bug Reports https://github.com/m-swirski/RiboCrypt/issues

Suggests testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19

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