:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-nanoporernaseq' .. highlight: bash bioconductor-nanoporernaseq =========================== .. conda:recipe:: bioconductor-nanoporernaseq :replaces_section_title: :noindex: Nanopore RNA\-Seq Example data :homepage: https://bioconductor.org/packages/3.18/data/experiment/html/NanoporeRNASeq.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-nanoporernaseq `_/`meta.yaml `_ The NanoporeRNASeq package contains long read RNA\-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines \(K562 and MCF7\) that were generated by the SG\-NEx project. Each of these cell lines has three replicates\, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 \(Grch38\) and stored as bam files. The original data is from the SG\-NEx project. .. conda:package:: bioconductor-nanoporernaseq |downloads_bioconductor-nanoporernaseq| |docker_bioconductor-nanoporernaseq| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-data-packages: ``>=20231203`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0`` :depends curl: :depends r-base: ``>=4.3,<4.4.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `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 `_ 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-nanoporernaseq and update with:: mamba update bioconductor-nanoporernaseq To create a new environment, run:: mamba create --name myenvname bioconductor-nanoporernaseq 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 quay.io/biocontainers/bioconductor-nanoporernaseq: (see `bioconductor-nanoporernaseq/tags`_ for valid values for ````) .. |downloads_bioconductor-nanoporernaseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-nanoporernaseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-nanoporernaseq :alt: (downloads) .. |docker_bioconductor-nanoporernaseq| image:: https://quay.io/repository/biocontainers/bioconductor-nanoporernaseq/status :target: https://quay.io/repository/biocontainers/bioconductor-nanoporernaseq .. _`bioconductor-nanoporernaseq/tags`: https://quay.io/repository/biocontainers/bioconductor-nanoporernaseq?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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-nanoporernaseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-nanoporernaseq/README.html