Package Recipe 'bioconductor-ribocrypt'

recipe bioconductor-ribocrypt

Interactive visualization in genomics

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/RiboCrypt.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-ribocrypt/meta.yaml

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.

package bioconductor-ribocrypt¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-orfik >=1.30.0,<1.31.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on r-base >=4.5,<4.6.0a0
on r-bslib
on r-cowplot
on r-crosstalk
on r-data.table
on r-dplyr
on r-dt
on r-fst
on r-ggplot2
on r-htmlwidgets
on r-httr
on r-jsonlite
on r-knitr
on r-markdown
on r-nglviewer
on r-plotly
on r-rclipboard
on r-rcurl
on r-rlang
on r-shiny
on r-shinycssloaders
on r-shinyhelper
on r-shinyjqui
on r-shinyjs
on r-shinywidgets
on r-stringr
on r-writexl

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-ribocrypt

to add into an existing workspace instead, run:

pixi add bioconductor-ribocrypt

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-ribocrypt

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ribocrypt

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-ribocrypt:<tag>

(see bioconductor-ribocrypt/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ribocrypt/README.html)