- recipe stream_atac
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data.
- Homepage:
- License:
AGPL-3
- Recipe:
- 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:
on anndata
on bioconductor-bsgenome.hsapiens.ucsc.hg19
on bioconductor-bsgenome.hsapiens.ucsc.hg38
on bioconductor-bsgenome.mmusculus.ucsc.mm10
on bioconductor-bsgenome.mmusculus.ucsc.mm9
on bioconductor-chromvar
on bioconductor-jaspar2016
on bioconductor-motifmatchr
on perl
on python
>=3on r-base
on r-essentials
on r-optparse
on rpy2
2.9.*on scikit-learn
on unzip
on wget
on zip
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install stream_atac
to add into an existing workspace instead, run:
pixi add stream_atac
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install stream_atac
Alternatively, to install into a new environment, run:
conda create -n envname stream_atac
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/stream_atac:<tag>
(see stream_atac/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/stream_atac/README.html)
