- recipe rsat-core
Regulatory Sequence Analysis Tools (RSAT)
- Homepage:
- License:
GNU Affero General Public License v3
- Recipe:
- Links:
biotools: rsat, doi: 10.1093/nar/gky317
Detection and analysis of regulatory signals in non-coding sequences.
- package 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:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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
myenvnamebeing 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:<tag> (see `rsat-core/tags`_ for valid values for ``<tag>``)
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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Link to this page¶
Render an 
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