recipe bioconductor-motif2site

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/Motif2Site.html

License:

GPL-2

Recipe:

/bioconductor-motif2site/meta.yaml

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

package bioconductor-motif2site

Versions:

1.2.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-edger >=3.40.0,<3.41.0

• 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-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-mass

• r-mixtools

Required By:

Installation

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

conda install bioconductor-motif2site

and update with:

conda update bioconductor-motif2site

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-motif2site:<tag>

(see bioconductor-motif2site/tags for valid values for <tag>)

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