recipe stream_atac

STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data.

Homepage:

https://github.com/pinellolab/STREAM_atac

License:

AGPL-3

Recipe:

/stream_atac/meta.yaml

package stream_atac

versions:

0.3.5-5,  0.3.5-4,  0.3.5-3,  0.3.5-2,  0.3.5-1,  0.3.5-0,  0.3.4-2,  0.3.4-1,  0.3.4-0, 

0.3.5-5,  0.3.5-4,  0.3.5-3,  0.3.5-2,  0.3.5-1,  0.3.5-0,  0.3.4-2,  0.3.4-1,  0.3.4-0,  0.3.3-0,  0.3.3a-0,  0.3.2-0,  0.3.1-1,  0.3.1-0,  0.3.0-0,  0.2.0-1,  0.2.0-0,  0.1.0-0

depends anndata:

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

depends bioconductor-bsgenome.hsapiens.ucsc.hg38:

depends bioconductor-bsgenome.mmusculus.ucsc.mm10:

depends bioconductor-bsgenome.mmusculus.ucsc.mm9:

depends bioconductor-chromvar:

depends bioconductor-jaspar2016:

depends bioconductor-motifmatchr:

depends perl:

depends python:

>=3

depends r-base:

depends r-essentials:

depends r-optparse:

depends rpy2:

2.9.*

depends scikit-learn:

depends unzip:

depends wget:

depends zip:

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 stream_atac

and update with::

   mamba update stream_atac

To create a new environment, run:

mamba create --name myenvname stream_atac

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/stream_atac:<tag>

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

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