Package Recipe 'bioconductor-enhancerhomologsearch'

recipe bioconductor-enhancerhomologsearch

Identification of putative mammalian orthologs to given enhancer

Homepage:: https://bioconductor.org/packages/3.20/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:

1.16.0-0, 1.12.0-0, 1.8.2-0, 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:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-biocfilecache >=3.0.0,<3.1.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-motifmatchr >=1.32.0,<1.33.0
on bioconductor-motifmatchr >=1.32.0,<1.33.0a0
on bioconductor-pwalign >=1.6.0,<1.7.0
on bioconductor-pwalign >=1.6.0,<1.7.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-httr
on r-jsonlite
on r-matrix
on r-rcpp

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-enhancerhomologsearch

to add into an existing workspace instead, run:

pixi add bioconductor-enhancerhomologsearch

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-enhancerhomologsearch

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-enhancerhomologsearch

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-enhancerhomologsearch:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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-enhancerhomologsearch/README.html)