recipe bioconductor-idr2d

Irreproducible Discovery Rate for Genomic Interactions Data

Homepage:

https://bioconductor.org/packages/3.18/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:

1.16.0-0,  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 bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=0.7.6

depends r-futile.logger:

>=1.4.3

depends r-ggplot2:

>=3.1.1

depends r-idr:

>=1.2

depends r-magrittr:

>=1.5

depends r-reticulate:

>=1.13

depends r-scales:

>=1.0.0

depends r-stringr:

>=1.3.1

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 bioconductor-idr2d

and update with::

   mamba update bioconductor-idr2d

To create a new environment, run:

mamba create --name myenvname bioconductor-idr2d

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/bioconductor-idr2d:<tag>

(see `bioconductor-idr2d/tags`_ for valid values for ``<tag>``)

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