:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-rnamodr' .. highlight: bash bioconductor-rnamodr ==================== .. conda:recipe:: bioconductor-rnamodr :replaces_section_title: :noindex: Detection of post\-transcriptional modifications in high throughput sequencing data :homepage: https://bioconductor.org/packages/3.18/bioc/html/RNAmodR.html :license: Artistic-2.0 :recipe: /`bioconductor-rnamodr `_/`meta.yaml `_ RNAmodR provides classes and workflows for loading\/aggregation data from high througput sequencing aimed at detecting post\-transcriptional modifications through analysis of specific patterns. In addition\, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package. .. conda:package:: bioconductor-rnamodr |downloads_bioconductor-rnamodr| |docker_bioconductor-rnamodr| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.2-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.0-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-gviz: ``>=1.46.0,<1.47.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-modstrings: ``>=1.18.0,<1.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-colorramps: :depends r-ggplot2: :depends r-matrixstats: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rocr: :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-rnamodr and update with:: mamba update bioconductor-rnamodr To create a new environment, run:: mamba create --name myenvname bioconductor-rnamodr 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-rnamodr: (see `bioconductor-rnamodr/tags`_ for valid values for ````) .. |downloads_bioconductor-rnamodr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-rnamodr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-rnamodr :alt: (downloads) .. |docker_bioconductor-rnamodr| image:: https://quay.io/repository/biocontainers/bioconductor-rnamodr/status :target: https://quay.io/repository/biocontainers/bioconductor-rnamodr .. _`bioconductor-rnamodr/tags`: https://quay.io/repository/biocontainers/bioconductor-rnamodr?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-rnamodr/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-rnamodr/README.html