:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-bamsignals' .. highlight: bash bioconductor-bamsignals ======================= .. conda:recipe:: bioconductor-bamsignals :replaces_section_title: :noindex: Extract read count signals from bam files :homepage: https://bioconductor.org/packages/3.18/bioc/html/bamsignals.html :license: GPL-2 :recipe: /`bioconductor-bamsignals `_/`meta.yaml `_ :links: biotools: :biotools:`bamsignals`, doi: :doi:`10.1038/nmeth.3252` This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired\-end data. .. conda:package:: bioconductor-bamsignals |downloads_bioconductor-bamsignals| |docker_bioconductor-bamsignals| :versions: .. raw:: html
1.34.0-01.32.0-01.30.0-11.30.0-01.26.0-21.26.0-11.26.0-01.24.0-01.22.0-1 ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.26.0-2``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :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-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0a0`` :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`` :depends r-rcpp: ``>=0.10.6`` :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-bamsignals and update with:: mamba update bioconductor-bamsignals To create a new environment, run:: mamba create --name myenvname bioconductor-bamsignals 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-bamsignals: (see `bioconductor-bamsignals/tags`_ for valid values for ````) .. |downloads_bioconductor-bamsignals| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-bamsignals.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-bamsignals :alt: (downloads) .. |docker_bioconductor-bamsignals| image:: https://quay.io/repository/biocontainers/bioconductor-bamsignals/status :target: https://quay.io/repository/biocontainers/bioconductor-bamsignals .. _`bioconductor-bamsignals/tags`: https://quay.io/repository/biocontainers/bioconductor-bamsignals?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-bamsignals/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-bamsignals/README.html