RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt  

Interactive visualization in genomics

Bioconductor version: Release (3.17)

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>

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")

 

HTML	R Script	RiboCrypt_app_tutorial.html
HTML	R Script	RiboCrypt_overview.html
PDF		Reference Manual
Text		LICENSE

Details

biocViews	RNASeq, RiboSeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 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
LinkingTo
Suggests	testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL	https://github.com/m-swirski/RiboCrypt
BugReports	https://github.com/m-swirski/RiboCrypt/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RiboCrypt_1.6.0.tar.gz
Windows Binary	RiboCrypt_1.6.0.zip (64-bit only)
macOS Binary (x86_64)	RiboCrypt_1.6.0.tgz
macOS Binary (arm64)	RiboCrypt_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RiboCrypt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RiboCrypt
Bioc Package Browser	https://code.bioconductor.org/browse/RiboCrypt/
Package Short Url	https://bioconductor.org/packages/RiboCrypt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive