Package Recipe 'bioconductor-nxtirfcore'

recipe bioconductor-nxtirfcore

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

Homepage:: https://bioconductor.org/packages/3.17/bioc/html/NxtIRFcore.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-nxtirfcore/meta.yaml

Interactively analyses Intron Retention and Alternative Splicing Events (ASE) in RNA-seq data. NxtIRF quantifies ASE events in BAM files aligned to the genome using a splice-aware aligner such as STAR. The core quantitation algorithm relies on the IRFinder/C++ engine ported via Rcpp for multi-platform compatibility. In addition, NxtIRF provides convenient pipelines for downstream analysis and publication-ready visualisation tools. Note that NxtIRFcore is now replaced by SpliceWiz in Bioconductor 3.16 onwards.

package bioconductor-nxtirfcore¶

Versions:

1.6.0-0, 1.4.0-1, 1.4.0-0, 1.0.0-2, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-annotationhub >=3.8.0,<3.9.0
on bioconductor-biocfilecache >=2.8.0,<2.9.0
on bioconductor-biocgenerics >=0.46.0,<0.47.0
on bioconductor-biocparallel >=1.34.0,<1.35.0
on bioconductor-biostrings >=2.68.0,<2.69.0
on bioconductor-bsgenome >=1.68.0,<1.69.0
on bioconductor-delayedarray >=0.26.0,<0.27.0
on bioconductor-delayedmatrixstats >=1.22.0,<1.23.0
on bioconductor-genefilter >=1.82.0,<1.83.0
on bioconductor-genomeinfodb >=1.36.0,<1.37.0
on bioconductor-genomicranges >=1.52.0,<1.53.0
on bioconductor-hdf5array >=1.28.0,<1.29.0
on bioconductor-iranges >=2.34.0,<2.35.0
on bioconductor-nxtirfdata >=1.6.0,<1.7.0
on bioconductor-rhdf5 >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.60.0,<1.61.0
on bioconductor-s4vectors >=0.38.0,<0.39.0
on bioconductor-summarizedexperiment >=1.30.0,<1.31.0
on bioconductor-zlibbioc >=1.46.0,<1.47.0
on libblas >=3.9.0,<4.0a0
on libgcc-ng >=12
on liblapack >=3.9.0,<4.0a0
on libstdcxx-ng >=12
on r-base >=4.3,<4.4.0a0
on r-data.table
on r-fst
on r-ggplot2
on r-magrittr
on r-plotly
on r-r.utils
on r-rcpp >=1.0.5
on r-rcppprogress

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-nxtirfcore

to add into an existing workspace instead, run:

pixi add bioconductor-nxtirfcore

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-nxtirfcore

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nxtirfcore

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-nxtirfcore:<tag>

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