Package Recipe 'bioconductor-nxtirfdata'

recipe bioconductor-nxtirfdata

Data for NxtIRF

Homepage:: https://bioconductor.org/packages/3.20/data/experiment/html/NxtIRFdata.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-nxtirfdata/meta.yaml

NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.

package bioconductor-nxtirfdata¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-data-packages >=20260207
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on curl
on r-base >=4.5,<4.6.0a0
on r-r.utils

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-nxtirfdata

to add into an existing workspace instead, run:

pixi add bioconductor-nxtirfdata

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-nxtirfdata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nxtirfdata

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-nxtirfdata:<tag>

(see bioconductor-nxtirfdata/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-nxtirfdata/README.html)