recipe bioconductor-greylistchip

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/GreyListChIP.html

License:

Artistic-2.0

Recipe:

/bioconductor-greylistchip/meta.yaml

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

Versions:

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0

Depends:

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-mass

Required By:

• bioconductor-diffbind

• bioconductor-epigrahmm

Installation

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

conda install bioconductor-greylistchip

and update with:

conda update bioconductor-greylistchip

or use the docker container:

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

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

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