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RiboCrypt

Interactive visualization in genomics


Bioconductor version: Release (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

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
See More
Suggests testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19
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Build Report Build Report

Package Archives

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

Source Package RiboCrypt_1.8.0.tar.gz
Windows Binary RiboCrypt_1.8.0.zip
macOS Binary (x86_64) RiboCrypt_1.8.0.tgz
macOS Binary (arm64) RiboCrypt_1.8.0.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