recipe cellbender

A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data

Homepage:

https://github.com/broadinstitute/CellBender

Documentation:

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

License:

BSD / BSD-3-Clause

Recipe:

/cellbender/meta.yaml

Links:

biotools: CellBender, doi: 10.1038/s41592-023-01943-7

package cellbender

versions:

0.3.2-0,  0.3.0-0

depends anndata:

>=0.7

depends ipython:

depends jupyter:

depends jupyter_contrib_nbextensions:

depends loompy:

depends matplotlib-base:

depends nbconvert:

<7.0.0

depends notebook:

<7.0.0

depends numpy:

depends pandas:

depends psutil:

depends pyro-ppl:

>=1.8.4

depends pytables:

depends python:

3.7.*

depends pytorch:

depends scipy:

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 cellbender

and update with::

   mamba update cellbender

To create a new environment, run:

mamba create --name myenvname cellbender

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/cellbender:<tag>

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

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