recipe repic

REPIC - an ensemble learning approach to cryo-EM particle picking.

Homepage:

https://github.com/ccameron/REPIC

Documentation:

https://repic.readthedocs.io/en/latest/

License:

BSD / BSD-3-Clause

Recipe:

/repic/meta.yaml

REliable PIcking by Consensus (REPIC) is an ensemble learning approach to cryogenic-electron microscopy (cryo-EM) particle picking. It identifies particles common to multiple picked particle sets (i.e., consensus particles) using graph theory and integer linear programming (ILP). Picked particle sets may be found by a human specialist (manual), template matching, mathematical function (e.g., RELION's Laplacian-of-Gaussian auto-picking), or machine-learning method. REPIC expects particle sets to be in BOX file format (*.box) where each particle has coordinates, a detection box size (in pixels), and (optional) a score [0-1].

package repic

(downloads) docker_repic

versions:

0.2.1-0,  0.2.0-0,  0.1.0-0,  0.0.0-0

depends matplotlib-base:

>=3.2.2

depends mrcfile:

>=1.4.3

depends networkx:

>=2.8.4

depends numpy:

>=1.24.2

depends pandas:

depends python:

>=3.8.16

depends scipy:

>=1.10.0

depends tqdm:

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 repic

and update with::

   mamba update repic

To create a new environment, run:

mamba create --name myenvname repic

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/repic:<tag>

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

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