- recipe pycistopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
- Homepage:
- License:
OTHER
- Recipe:
- package pycistopic¶
- versions:
2.0a-0- depends adjusttext:
- depends bbknn:
- depends bs4:
- depends gensim:
- depends harmonypy:
- depends igraph:
- depends leidenalg:
- depends loomxpy:
- depends lxml:
- depends macs2:
- depends matplotlib-base:
<3.7- depends numpy:
>=1.20.3- depends pandas:
>=1.5,<2- depends polars:
>=0.18.3- depends pyarrow:
>=8.0.0- depends pybiomart:
- depends pyranges:
<0.0.128- depends pyscenic:
- depends python:
>=3.9- depends ray-default:
- depends scanorama:
- depends scanpy:
- depends scatac-fragment-tools:
- depends scikit-learn:
- depends scrublet:
- depends seaborn:
- depends statsmodels:
- depends tmtoolkit:
- 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 pycistopic and update with:: mamba update pycistopic
To create a new environment, run:
mamba create --name myenvname pycistopic
with
myenvnamebeing 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/pycistopic:<tag> (see `pycistopic/tags`_ for valid values for ``<tag>``)
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Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pycistopic/README.html)
