recipe bioconductor-deltacapturec

This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/deltaCaptureC.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-deltacapturec/meta.yaml

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

package bioconductor-deltacapturec

(downloads) docker_bioconductor-deltacapturec

Versions:
1.24.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0, 

1.24.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends:

  • on bioconductor-deseq2 >=1.50.0,<1.51.0

  • on bioconductor-genomicranges >=1.62.0,<1.63.0

  • on bioconductor-iranges >=2.44.0,<2.45.0

  • on bioconductor-summarizedexperiment >=1.40.0,<1.41.0

  • on r-base >=4.5,<4.6.0a0

  • on r-ggplot2

  • on r-tictoc

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 bioconductor-deltacapturec

to add into an existing workspace instead, run:

pixi add bioconductor-deltacapturec

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 bioconductor-deltacapturec

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-deltacapturec

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/bioconductor-deltacapturec:<tag>

(see bioconductor-deltacapturec/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.

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Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-deltacapturec/README.html)