recipe schicexplorer

Set of programs to process, analyze and visualize single-cell Hi-C data.

Homepage:

https://github.com/joachimwolff/scHiCExplorer

License:

GPL3

Recipe:

/schicexplorer/meta.yaml

package schicexplorer

versions:

7-0,  6-0,  5-0,  4-0,  3-0,  2-0,  1-0

depends cooler:

>=0.8.10

depends hicexplorer:

>=3.6

depends hicmatrix:

>=15

depends holoviews:

depends hyperopt:

depends matplotlib-base:

depends numpy:

>=1.18

depends python:

>3

depends scikit-learn:

>=0.22

depends scipy:

>=1.4

depends sparse-neighbors-search:

>=0.7

depends umap-learn:

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 schicexplorer

and update with::

   mamba update schicexplorer

To create a new environment, run:

mamba create --name myenvname schicexplorer

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/schicexplorer:<tag>

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

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