:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-extrachips' .. highlight: bash bioconductor-extrachips ======================= .. conda:recipe:: bioconductor-extrachips :replaces_section_title: :noindex: Additional functions for working with ChIP\-Seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/extraChIPs.html :license: GPL-3 :recipe: /`bioconductor-extrachips `_/`meta.yaml `_ This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP\-Seq data. The focus is on detecting differential binding windows\/regions. One set of functions focusses on set\-operations retaining mcols for GRanges objects\, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also included. .. conda:package:: bioconductor-extrachips |downloads_bioconductor-extrachips| |docker_bioconductor-extrachips| :versions: ``1.6.0-0``,  ``1.4.5-0``,  ``1.2.0-0`` :depends bioconductor-biocio: ``>=1.12.0,<1.13.0`` :depends bioconductor-biocio: ``>=1.12.0,<1.13.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-csaw: ``>=1.36.0,<1.37.0`` :depends bioconductor-csaw: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-edger: ``>=4.0.2,<4.1.0a0`` :depends bioconductor-enrichedheatmap: ``>=1.32.0,<1.33.0`` :depends bioconductor-enrichedheatmap: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicinteractions: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomicinteractions: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-gviz: ``>=1.46.0,<1.47.0`` :depends bioconductor-gviz: ``>=1.46.1,<1.47.0a0`` :depends bioconductor-interactionset: ``>=1.30.0,<1.31.0`` :depends bioconductor-interactionset: ``>=1.30.0,<1.31.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :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-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-broom: :depends r-complexupset: :depends r-dplyr: ``>=1.1.1`` :depends r-forcats: :depends r-ggforce: :depends r-ggplot2: ``>=3.4.0`` :depends r-ggrepel: :depends r-ggside: ``>=0.2.2`` :depends r-glue: :depends r-matrixstats: :depends r-patchwork: :depends r-rcolorbrewer: :depends r-rlang: :depends r-scales: :depends r-stringr: :depends r-tibble: :depends r-tidyr: :depends r-tidyselect: :depends r-vctrs: :depends r-venndiagram: :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-extrachips and update with:: mamba update bioconductor-extrachips To create a new environment, run:: mamba create --name myenvname bioconductor-extrachips 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-extrachips: (see `bioconductor-extrachips/tags`_ for valid values for ````) .. |downloads_bioconductor-extrachips| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-extrachips.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-extrachips :alt: (downloads) .. |docker_bioconductor-extrachips| image:: https://quay.io/repository/biocontainers/bioconductor-extrachips/status :target: https://quay.io/repository/biocontainers/bioconductor-extrachips .. _`bioconductor-extrachips/tags`: https://quay.io/repository/biocontainers/bioconductor-extrachips?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-extrachips/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-extrachips/README.html