recipe bioconductor-mmdiff2

Statistical Testing for ChIP-Seq data sets

Homepage

https://bioconductor.org/packages/3.12/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

1.18.0-0,  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 >=2.50.0,<2.51.0

• bioconductor-biostrings >=2.58.0,<2.59.0

• bioconductor-bsgenome >=1.58.0,<1.59.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-rsamtools >=2.6.0,<2.7.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• 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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