recipe bioconductor-regionreport

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-regionreport/meta.yaml

Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.

package bioconductor-regionreport

versions:

1.36.0-0,  1.34.0-0,  1.32.0-0,  1.27.1-0,  1.26.0-0,  1.24.2-0,  1.24.0-0,  1.22.0-0,  1.20.0-0, 

1.36.0-0,  1.34.0-0,  1.32.0-0,  1.27.1-0,  1.26.0-0,  1.24.2-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.2-0,  1.16.1-0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-deformats:

>=1.30.0,<1.31.0

depends bioconductor-derfinder:

>=1.36.0,<1.37.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-knitr:

>=1.6

depends r-knitrbootstrap:

>=0.9.0

depends r-refmanager:

depends r-rmarkdown:

>=0.9.5

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-regionreport

and update with::

   mamba update bioconductor-regionreport

To create a new environment, run:

mamba create --name myenvname bioconductor-regionreport

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-regionreport:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-regionreport/README.html)