:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-quasr' .. highlight: bash bioconductor-quasr ================== .. conda:recipe:: bioconductor-quasr :replaces_section_title: :noindex: Quantify and Annotate Short Reads in R :homepage: https://bioconductor.org/packages/3.18/bioc/html/QuasR.html :license: GPL-2 :recipe: /`bioconductor-quasr `_/`meta.yaml `_ :links: biotools: :biotools:`quasr` This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads\, over creation of alignments and quality control plots\, to the quantification of genomic regions of interest. .. conda:package:: bioconductor-quasr |downloads_bioconductor-quasr| |docker_bioconductor-quasr| :versions: .. raw:: html
1.42.1-01.40.1-01.38.0-11.38.0-01.34.0-21.34.0-11.34.0-01.32.0-01.30.0-2 ``1.42.1-0``,  ``1.40.1-0``,  ``1.38.0-1``,  ``1.38.0-0``,  ``1.34.0-2``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-2``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.2-0``,  ``1.22.1-0``,  ``1.20.0-0``,  ``1.18.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-bsgenome: ``>=1.70.1,<1.71.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfeatures: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-genomicfiles: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicfiles: ``>=1.38.0,<1.39.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-rbowtie: ``>=1.42.0,<1.43.0`` :depends bioconductor-rbowtie: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-shortread: ``>=1.60.0,<1.61.0`` :depends bioconductor-shortread: ``>=1.60.0,<1.61.0a0`` :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`` :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-quasr and update with:: mamba update bioconductor-quasr To create a new environment, run:: mamba create --name myenvname bioconductor-quasr 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-quasr: (see `bioconductor-quasr/tags`_ for valid values for ````) .. |downloads_bioconductor-quasr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-quasr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-quasr :alt: (downloads) .. |docker_bioconductor-quasr| image:: https://quay.io/repository/biocontainers/bioconductor-quasr/status :target: https://quay.io/repository/biocontainers/bioconductor-quasr .. _`bioconductor-quasr/tags`: https://quay.io/repository/biocontainers/bioconductor-quasr?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-quasr/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-quasr/README.html