recipe bioconductor-spatzie

Identification of enriched motif pairs from chromatin interaction data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-spatzie/meta.yaml

Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.

package bioconductor-spatzie

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicinteractions:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-motifmatchr:

>=1.24.0,<1.25.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-tfbstools:

>=1.40.0,<1.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-matrixstats:

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-spatzie

and update with::

   mamba update bioconductor-spatzie

To create a new environment, run:

mamba create --name myenvname bioconductor-spatzie

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-spatzie:<tag>

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

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