recipe chexalign

ChExAlign is used for alignment and quantification of ChIP-exo crosslinking patterns.

Homepage:

https://github.com/seqcode/chexalign

License:

MIT

Recipe:

/chexalign/meta.yaml

ChExAlign is a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. The output of the alignment approach is a set of composite profiles that represent the crosslinking signatures of the complex across analyzed regulatory regions. We then use a probabilistic mixture model to deconvolve individual crosslinking events within the aligned ChIP-exo profiles, enabling consistent measurements of protein-DNA crosslinking strengths across multiple proteins.

package chexalign

(downloads) docker_chexalign

versions:

0.12-1,  0.12-0,  0.11-0

depends openjdk:

>=8

requirements:

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 chexalign

and update with::

   mamba update chexalign

To create a new environment, run:

mamba create --name myenvname chexalign

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/chexalign:<tag>

(see `chexalign/tags`_ for valid values for ``<tag>``)

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Link to this page

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