Package Recipe 'bioconductor-idr2d'

recipe bioconductor-idr2d

Irreproducible Discovery Rate for Genomic Interactions Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/idr2d.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-idr2d/meta.yaml

A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.

package bioconductor-idr2d¶

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, 1.2.2-0, 1.0.0-0

Depends:

on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on r-base >=4.5,<4.6.0a0
on r-dplyr >=0.7.6
on r-futile.logger >=1.4.3
on r-ggplot2 >=3.1.1
on r-idr >=1.2
on r-magrittr >=1.5
on r-reticulate >=1.13
on r-scales >=1.0.0
on r-stringr >=1.3.1

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-idr2d

to add into an existing workspace instead, run:

pixi add bioconductor-idr2d

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-idr2d

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-idr2d

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-idr2d:<tag>

(see bioconductor-idr2d/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-idr2d/README.html)