recipe bioconductor-ctcf

Genomic coordinates of CTCF binding sites, with orientation

Homepage:

https://bioconductor.org/packages/3.20/data/annotation/html/CTCF.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-ctcf/meta.yaml

Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. CTCF sites obtained using JASPAR's MA0139.1 PWM and filtered at 1e-6 p-value threshold are recommended.

package bioconductor-ctcf

(downloads) docker_bioconductor-ctcf

versions:

0.99.11-2,  0.99.11-1,  0.99.11-0,  0.99.9-0,  0.99.4-1,  0.99.4-0

depends bioconductor-data-packages:

>=20241103

depends curl:

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-ctcf

and update with::

   mamba update bioconductor-ctcf

To create a new environment, run:

mamba create --name myenvname bioconductor-ctcf

with myenvname being 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-ctcf:<tag>

(see `bioconductor-ctcf/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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