recipe bioconductor-chipseqr

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/ChIPseqR.html

License:

GPL (>= 2)

Recipe:

/bioconductor-chipseqr/meta.yaml

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

package bioconductor-chipseqr

versions:

1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1, 

1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.36.0-1,  1.36.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-hilbertvis:

>=1.60.0,<1.61.0

depends bioconductor-hilbertvis:

>=1.60.0,<1.61.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0a0

depends libblas:

>=3.9.0,<4.0a0

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-fbasics:

depends r-timsac:

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-chipseqr

and update with::

   mamba update bioconductor-chipseqr

To create a new environment, run:

mamba create --name myenvname bioconductor-chipseqr

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-chipseqr:<tag>

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

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