recipe cellqc

Cellqc standardizes the qualiy control of single-cell RNA-Seq (scRNA) data to render clean feature count matrices.

Homepage:

https://github.com/lijinbio/cellqc

License:

MIT / MIT

Recipe:

/cellqc/meta.yaml

package cellqc

versions:

0.0.7-0,  0.0.6-1,  0.0.6-0,  0.0.4-1,  0.0.4-0,  0.0.3-0

depends anndata:

0.7.8.*

depends bioconductor-dropletutils:

depends click:

depends graphviz:

>=9.0.0,<10.0a0

depends numpy:

depends pygraphviz:

depends python:

depends r-dplyr:

depends r-ggplot2:

depends r-harmony:

depends r-remotes:

depends r-scpred:

depends r-seurat:

depends r-seuratobject:

depends r-soupx:

>=1.6.2

depends scanpy:

>=1.9.1

depends snakemake:

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 cellqc

and update with::

   mamba update cellqc

To create a new environment, run:

mamba create --name myenvname cellqc

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/cellqc:<tag>

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

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