:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'rsat-core' .. highlight: bash rsat-core ========= .. conda:recipe:: rsat-core :replaces_section_title: :noindex: Regulatory Sequence Analysis Tools \(RSAT\) :homepage: http://rsat.eu :license: GNU Affero General Public License v3 :recipe: /`rsat-core `_/`meta.yaml `_ :links: biotools: :biotools:`rsat`, doi: :doi:`10.1093/nar/gky317` Detection and analysis of regulatory signals in non\-coding sequences. .. conda:package:: rsat-core |downloads_rsat-core| |docker_rsat-core| :versions: ``2025.04.04-0``,  ``2020.02.29-1``,  ``2020.02.29-0``,  ``2020.02.28-0``,  ``2020.01.04-0`` :depends bedtools: :depends bioconductor-ctc: :depends bioconductor-qvalue: :depends blast: :depends d3: :depends ghostscript: :depends gnuplot: :depends httplib2: :depends libgcc: ``>=13`` :depends libgfortran: :depends libgfortran5: ``>=13.3.0`` :depends libstdcxx: ``>=13`` :depends matplotlib-base: :depends numpy: :depends opencv: :depends perl: :depends perl-algorithm-cluster: :depends perl-app-cpanminus: :depends perl-bio-das: :depends perl-bioperl: :depends perl-cgi: :depends perl-class-std-fast: :depends perl-data-dumper: :depends perl-db_file: :depends perl-dbd-mysql: :depends perl-dbi: :depends perl-digest-md5-file: :depends perl-email-simple: :depends perl-ensembl-api: :depends perl-ensembl-genomes: :depends perl-file-spec: :depends perl-gd: :depends perl-http-tiny: :depends perl-io-all: :depends perl-json: :depends perl-lockfile-simple: :depends perl-log-log4perl: :depends perl-lwp-simple: :depends perl-math-cdf: :depends perl-mce-shared: :depends perl-number-format: :depends perl-object-insideout: :depends perl-parallel-forkmanager: :depends perl-posix: :depends perl-postscript-simple: :depends perl-readonly: :depends perl-rest-client: :depends perl-soap-lite: :depends perl-statistics-distributions: :depends perl-util-properties: :depends perl-xml-dom: :depends perl-xml-libxml: :depends perl-xml-parser: :depends perl-yaml: :depends pygraphviz: :depends python: :depends pyyaml: :depends r-amap: :depends r-base: :depends r-data.table: :depends r-dendextend: :depends r-devtools: :depends r-dplyr: :depends r-dynamictreecut: :depends r-egg: :depends r-flux: :depends r-ggplot2: :depends r-gplots: :depends r-gridextra: :depends r-jpeg: :depends r-png: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rjsonio: :depends r-zoo: :depends scipy: :depends seqlogo: :depends snakemake: :depends vmatch: :depends weblogo: :requirements: :additional platforms: .. 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 rsat-core and update with:: mamba update rsat-core To create a new environment, run:: mamba create --name myenvname rsat-core 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/rsat-core: (see `rsat-core/tags`_ for valid values for ````) .. |downloads_rsat-core| image:: https://img.shields.io/conda/dn/bioconda/rsat-core.svg?style=flat :target: https://anaconda.org/bioconda/rsat-core :alt: (downloads) .. |docker_rsat-core| image:: https://quay.io/repository/biocontainers/rsat-core/status :target: https://quay.io/repository/biocontainers/rsat-core .. _`rsat-core/tags`: https://quay.io/repository/biocontainers/rsat-core?tab=tags .. raw:: html Notes ----- This package installs RSAT tools to analyse cis\-regulatory elements\, supporting\: \* motif discovery \(support genome\-wide data sets like ChIP\-seq\) \* transcription factor binding motif analysis \(quality assessment\, comparisons and clustering\) \* comparative genomics \* analysis of regulatory variations Documentation can be found at https\:\/\/rsa\-tools.github.io\/installing\-RSAT Note that this package does not include genome sequences nor DNA motif collections\, please check https\:\/\/rsa\-tools.github.io\/installing\-RSAT\/RSAT\-Docker\/RSAT\-Docker\-tuto.html to learn how to add them in your system. 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