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RiboCrypt

This is the development version of RiboCrypt; for the stable release version, see RiboCrypt.

Interactive visualization in genomics

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews RNASeq, RiboSeq, Sequencing, Software
Version 1.7.0
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
Linking To
Suggests testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19
System Requirements
Enhances
URL https://github.com/m-swirski/RiboCrypt
Bug Reports https://github.com/m-swirski/RiboCrypt/issues
See More
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_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64) RiboCrypt_1.7.0.tgz
macOS Binary (arm64)
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