recipe bioconductor-greylistchip

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs






Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.

package bioconductor-greylistchip

(downloads) docker_bioconductor-greylistchip



depends bioconductor-bsgenome:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicalignments:


depends bioconductor-genomicranges:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-mass:



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-greylistchip

and update with::

   mamba update bioconductor-greylistchip

To create a new environment, run:

mamba create --name myenvname bioconductor-greylistchip

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<tag>

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

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