recipe bioconductor-spatzie

Identification of enriched motif pairs from chromatin interaction data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-spatzie/meta.yaml

Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.

package bioconductor-spatzie

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicinteractions >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-motifmatchr >=1.20.0,<1.21.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-tfbstools >=1.36.0,<1.37.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-matrixstats

Required By:

Installation

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

conda install bioconductor-spatzie

and update with:

conda update bioconductor-spatzie

or use the docker container:

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

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

Download stats

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