- recipe bioconductor-sevenc
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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¶
- depends bioconductor-biocgenerics:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-interactionset:
- depends bioconductor-iranges:
- depends bioconductor-rtracklayer:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-boot:
- depends r-data.table:
- depends r-purrr:
- depends r-readr:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-sevenc and update with:: mamba update bioconductor-sevenc
To create a new environment, run:
mamba create --name myenvname bioconductor-sevenc
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-sevenc:<tag> (see `bioconductor-sevenc/tags`_ for valid values for ``<tag>``)