recipe bioconductor-nxtirfcore

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






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

(downloads) docker_bioconductor-nxtirfcore



depends bioconductor-annotationhub:


depends bioconductor-biocfilecache:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-bsgenome:


depends bioconductor-delayedarray:


depends bioconductor-delayedmatrixstats:


depends bioconductor-genefilter:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-hdf5array:


depends bioconductor-iranges:


depends bioconductor-nxtirfdata:


depends bioconductor-rhdf5:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-zlibbioc:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-data.table:

depends r-fst:

depends r-ggplot2:

depends r-magrittr:

depends r-plotly:

depends r-r.utils:

depends r-rcpp:


depends r-rcppprogress:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here 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 for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

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