recipe bioconductor-chipxpress

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

Homepage:

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

License:

GPL(>=2)

Recipe:

/bioconductor-chipxpress/meta.yaml

Links:

biotools: chipxpress, doi: 10.1186/1471-2105-14-188

ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

package bioconductor-chipxpress

versions:

1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.30.0-1,  1.28.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0

depends bioconductor-affy:

>=1.76.0,<1.77.0

depends bioconductor-biobase:

>=2.58.0,<2.59.0

depends bioconductor-chipxpressdata:

>=1.36.0,<1.37.0

depends bioconductor-frma:

>=1.50.0,<1.51.0

depends bioconductor-geoquery:

>=2.66.0,<2.67.0

depends r-base:

>=4.2,<4.3.0a0

depends r-biganalytics:

depends r-bigmemory:

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-chipxpress

and update with::

   mamba update bioconductor-chipxpress

To create a new environment, run:

mamba create --name myenvname bioconductor-chipxpress

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-chipxpress:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-chipxpress/README.html)