recipe bioconductor-cogito

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/Cogito.html

License:

LGPL-3

Recipe:

/bioconductor-cogito/meta.yaml

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

package bioconductor-cogito

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.mmusculus.ucsc.mm9.knowngene:

>=3.2.0,<3.3.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-entropy:

depends r-ggplot2:

depends r-jsonlite:

depends r-magrittr:

depends r-rmarkdown:

requirements:

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 bioconductor-cogito

and update with::

   mamba update bioconductor-cogito

To create a new environment, run:

mamba create --name myenvname bioconductor-cogito

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-cogito:<tag>

(see `bioconductor-cogito/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an badge with the following MarkDown:

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