recipe cite-seq-count

A python package to map reads from CITE-seq or hashing data for single cell experiments.

Homepage:

https://hoohm.github.io/CITE-seq-Count

Developer docs:

https://github.com/Hoohm/CITE-seq-Count

License:

MIT / MIT

Recipe:

/cite-seq-count/meta.yaml

Links:

biotools: CITE-seq-Count, usegalaxy-eu: cite_seq_count, doi: 10.5281/zenodo.2590196

package cite-seq-count

versions:

1.4.5-0,  1.4.4-0

depends multiprocess:

>=0.70.6.1

depends pandas:

>=0.23.4

depends pybktree:

1.1

depends pytest:

depends pytest-dependency:

depends python:

>=3.6

depends python-levenshtein:

>=0.12.0

depends scipy:

>=1.1.0

depends umi_tools:

>=1.1.5

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 cite-seq-count

and update with::

   mamba update cite-seq-count

To create a new environment, run:

mamba create --name myenvname cite-seq-count

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/cite-seq-count:<tag>

(see `cite-seq-count/tags`_ for valid values for ``<tag>``)

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