recipe paralyzer

We developed the PARalyzer algorithm to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol.The use of photoactivatable nucleotides in the PAR-CLIP protocol results in more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking, providing for single-nucleotide resolution binding information. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

Homepage:

https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/

License:

PARalyzer is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.

Recipe:

/paralyzer/meta.yaml

Links:

biotools: paralyzer

package paralyzer

(downloads) docker_paralyzer

versions:

1.5-3,  1.5-2,  1.5-1,  1.5-0

depends openjdk:

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 paralyzer

and update with::

   mamba update paralyzer

To create a new environment, run:

mamba create --name myenvname paralyzer

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/paralyzer:<tag>

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

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Link to this page

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