recipe bioconductor-mmdiff2

Statistical Testing for ChIP-Seq data sets

Homepage

https://bioconductor.org/packages/3.11/bioc/html/MMDiff2.html

License

Artistic-2.0

Recipe

/bioconductor-mmdiff2/meta.yaml

Links

biotools: mmdiff2, doi: 10.1038/nmeth.3252

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

package bioconductor-mmdiff2

Versions

1.16.0-0, 1.14.0-0, 1.12.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-locfit

• r-rcolorbrewer

• r-shiny

Required By

Installation

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

conda install bioconductor-mmdiff2

and update with:

conda update bioconductor-mmdiff2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-mmdiff2:<tag>

(see bioconductor-mmdiff2/tags for valid values for <tag>)

Link to this page

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