recipe chexmix

ChExMix aims to characterize protein-DNA binding subtypes in ChIP-exo experiments. ChExMix assumes that different regulatory complexes will result in different protein-DNA crosslinking signatures in ChIP-exo data, and thus analysis of ChIP-exo sequencing tag patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. ChExMix uses a mixture modeling framework to probabilistically model the genomic locations and subtype membership of protein-DNA binding events, leveraging both ChIP-exo tag enrichment patterns and DNA sequence information. In doing so, ChExMix offers a more principled and robust approach to characterizing binding subtypes than simply clustering binding events using motif information.

Homepage:

http://mahonylab.org/software/chexmix/

License:

MIT

Recipe:

/chexmix/meta.yaml

package chexmix

(downloads) docker_chexmix

versions:

0.52-0,  0.51-0,  0.45-0,  0.5-1,  0.5-0,  0.4-0

depends meme:

>=4.11.2

depends openjdk:

>=8

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 chexmix

and update with::

   mamba update chexmix

To create a new environment, run:

mamba create --name myenvname chexmix

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/chexmix:<tag>

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

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