:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-riboprofiling' .. highlight: bash bioconductor-riboprofiling ========================== .. conda:recipe:: bioconductor-riboprofiling :replaces_section_title: :noindex: Ribosome Profiling Data Analysis\: from BAM to Data Representation and Interpretation :homepage: https://bioconductor.org/packages/3.18/bioc/html/RiboProfiling.html :license: GPL-3 :recipe: /`bioconductor-riboprofiling `_/`meta.yaml `_ :links: biotools: :biotools:`riboprofiling`, doi: :doi:`10.12688/f1000research.8964.1` Starting with a BAM file\, this package provides the necessary functions for quality assessment\, read start position recalibration\, the counting of reads on CDS\, 3\'UTR\, and 5\'UTR\, plotting of count data\: pairs\, log fold\-change\, codon frequency and coverage assessment\, principal component analysis on codon coverage. .. conda:package:: bioconductor-riboprofiling |downloads_bioconductor-riboprofiling| |docker_bioconductor-riboprofiling| :versions: .. raw:: html
1.32.0-01.30.0-01.28.0-01.24.0-01.22.0-01.20.0-11.20.0-01.18.0-01.16.0-0 ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.7.1-0``,  ``1.6.0-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :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-ggbio: ``>=1.50.0,<1.51.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :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-data.table: :depends r-ggplot2: :depends r-plyr: :depends r-reshape2: :depends r-sqldf: :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-riboprofiling and update with:: mamba update bioconductor-riboprofiling To create a new environment, run:: mamba create --name myenvname bioconductor-riboprofiling 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-riboprofiling: (see `bioconductor-riboprofiling/tags`_ for valid values for ````) .. |downloads_bioconductor-riboprofiling| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-riboprofiling.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-riboprofiling :alt: (downloads) .. |docker_bioconductor-riboprofiling| image:: https://quay.io/repository/biocontainers/bioconductor-riboprofiling/status :target: https://quay.io/repository/biocontainers/bioconductor-riboprofiling .. _`bioconductor-riboprofiling/tags`: https://quay.io/repository/biocontainers/bioconductor-riboprofiling?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-riboprofiling/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-riboprofiling/README.html