:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'bioconductor-nxtirfcore'
.. highlight: bash

bioconductor-nxtirfcore
=======================

.. conda:recipe:: bioconductor-nxtirfcore
   :replaces_section_title:
   :noindex:

   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 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-nxtirfcore>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/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.


.. conda:package:: bioconductor-nxtirfcore

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

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
  We will show all commands using mamba below, but the arguments are the same for the two
  others.

  Given that you already have a conda environment in which you want to have this package, install with::

      mamba install bioconductor-nxtirfcore

   and update with::

      mamba update bioconductor-nxtirfcore

  To create a new environment, run::

      mamba create --name myenvname bioconductor-nxtirfcore

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

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

   (see `bioconductor-nxtirfcore/tags`_ for valid values for ``<tag>``)


.. |downloads_bioconductor-nxtirfcore| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-nxtirfcore.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-nxtirfcore
   :alt:   (downloads)
.. |docker_bioconductor-nxtirfcore| image:: https://quay.io/repository/biocontainers/bioconductor-nxtirfcore/status
   :target: https://quay.io/repository/biocontainers/bioconductor-nxtirfcore
.. _`bioconductor-nxtirfcore/tags`: https://quay.io/repository/biocontainers/bioconductor-nxtirfcore?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-nxtirfcore";
        var versions = ["1.6.0","1.4.0","1.4.0","1.0.0","1.0.0"];
    </script>






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