recipe bioconductor-sevenc

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Homepage

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

License

GPL-3

Recipe

/bioconductor-sevenc/meta.yaml

Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.

package bioconductor-sevenc

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-interactionset >=1.16.0,<1.17.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-boot >=1.3-20

• r-data.table >=1.10.4

• r-purrr >=0.2.2

• r-readr >=1.1.0

Required By

Installation

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

conda install bioconductor-sevenc

and update with:

conda update bioconductor-sevenc

or use the docker container:

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

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

Link to this page

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