recipe bioconductor-basicstarrseq

Basic peak calling on STARR-seq data

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-basicstarrseq/meta.yaml

Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.

package bioconductor-basicstarrseq

(downloads) docker_bioconductor-basicstarrseq

versions:
1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-1,  1.10.0-0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

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-basicstarrseq

and update with::

   mamba update bioconductor-basicstarrseq

To create a new environment, run:

mamba create --name myenvname bioconductor-basicstarrseq

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-basicstarrseq:<tag>

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

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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-basicstarrseq/README.html)