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/3.14/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

1.38.0-0,  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 >=1.72.0,<1.73.0

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-chipxpressdata >=1.32.0,<1.33.0

• bioconductor-frma >=1.46.0,<1.47.0

• bioconductor-geoquery >=2.62.0,<2.63.0

• r-base >=4.1,<4.2.0a0

• r-biganalytics

• r-bigmemory

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-chipxpress

and update with:

conda update bioconductor-chipxpress

or use the docker container:

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

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

Download stats

Link to this page

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