recipe bioconductor-enhancerhomologsearch

Identification of putative mammalian orthologs to given enhancer

Homepage:

https://bioconductor.org/packages/3.16/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:

1.4.0-0,  1.0.1-0,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-biocfilecache >=2.6.0,<2.7.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-motifmatchr >=1.20.0,<1.21.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-httr

• r-jsonlite

• r-matrix

• r-rcpp

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-enhancerhomologsearch

and update with:

conda update bioconductor-enhancerhomologsearch

or 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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