recipe hicexplorer

Set of programs to process, analyze and visualize Hi-C and capture Hi-C data

Homepage:

https://github.com/deeptools/HiCExplorer

Documentation:

https://hicexplorer.readthedocs.org/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/hicexplorer/meta.yaml

Links:

doi: 10.1093/nar/gky504, doi: 10.1093/nar/gkaa220, doi: 10.1093/gigascience/giac061, usegalaxy-eu: hicexplorer_hicplotviewpoint, biotools: hicexplorer

package hicexplorer

versions:

3.7.6-0,  3.7.5-0,  3.7.4-0,  3.7.3-1,  3.7.3-0,  3.7.2-1,  3.7.2-0,  3.7.1-0,  3.7-0, 

3.7.6-0,  3.7.5-0,  3.7.4-0,  3.7.3-1,  3.7.3-0,  3.7.2-1,  3.7.2-0,  3.7.1-0,  3.7-0,  3.6-0,  3.5.3-0,  3.5.2-0,  3.5.1-0,  3.5-0,  3.4.3-1,  3.4.3-0,  3.4.2-0,  3.4.1-1,  3.4.1-0,  3.4-0,  3.3.1-0,  3.3-0,  3.2-0,  3.1-0,  3.0.2-0,  3.0.1-0,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2-1,  2.2-0,  2.2beta-0,  2.1.4-3,  2.1.4-2,  2.1.3-0,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.1-0,  2.1alpha1-0,  2.0-1,  2.0-0,  1.8.1-0,  1.8-2,  1.8-1,  1.8-0,  1.7.2-0,  1.7.1-0,  1.6.1-0,  1.6-0,  1.4-0,  1.3-0,  1.2-0,  1.1a-0,  0.1-0

depends biopython:

depends cleanlab:

>=2.5

depends cooler:

>=0.9.3

depends fit_nbinom:

>=1.2

depends future:

depends hic2cool:

>=0.8.3

depends hicmatrix:

>=17

depends hyperopt:

>=0.2.7

depends imbalanced-learn:

>=0.11

depends intervaltree:

depends ipykernel:

>=6.25.2

depends jinja2:

depends krbalancing:

>=0.0.5

depends matplotlib-base:

>=3.6

depends numpy:

>=1.19

depends pandas:

>=2.0

depends psutil:

depends pybedtools:

>=0.9

depends pybigwig:

depends pygenometracks:

>=3.8

depends pysam:

depends pytables:

depends python:

>=3.8

depends python-graphviz:

>=0.20

depends scikit-learn:

>=1.3,<1.4

depends scipy:

>=1.10

depends tqdm:

>=4.66

depends unidecode:

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 hicexplorer

and update with::

   mamba update hicexplorer

To create a new environment, run:

mamba create --name myenvname hicexplorer

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/hicexplorer:<tag>

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

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