recipe bioconductor-nullranges

Generation of null ranges via bootstrapping or covariate matching

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/nullranges.html

License:

GPL-3

Recipe:

/bioconductor-nullranges/meta.yaml

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

package bioconductor-nullranges

versions:

1.6.2-0,  1.4.0-0,  1.0.0-0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-interactionset:

>=1.28.0,<1.29.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-plyranges:

>=1.20.0,<1.21.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

depends r-ggridges:

depends r-progress:

depends r-rlang:

depends r-scales:

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-nullranges

and update with::

   mamba update bioconductor-nullranges

To create a new environment, run:

mamba create --name myenvname bioconductor-nullranges

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-nullranges:<tag>

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

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