recipe bioconductor-enhancerhomologsearch

Identification of putative mammalian orthologs to given enhancer

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-enhancerhomologsearch/meta.yaml

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

package bioconductor-enhancerhomologsearch

versions:

1.6.1-0,  1.4.0-1,  1.4.0-0,  1.0.1-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-motifmatchr:

>=1.22.0,<1.23.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-httr:

depends r-jsonlite:

depends r-matrix:

depends r-rcpp:

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-enhancerhomologsearch

and update with::

   mamba update bioconductor-enhancerhomologsearch

To create a new environment, run:

mamba create --name myenvname bioconductor-enhancerhomologsearch

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-enhancerhomologsearch:<tag>

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

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