recipe bioconductor-degcre

Probabilistic association of DEGs to CREs from differential data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-degcre/meta.yaml

DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

package bioconductor-degcre

versions:

1.2.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-interactionset:

>=1.34.0,<1.35.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-org.hs.eg.db:

>=3.20.0,<3.21.0

depends bioconductor-plotgardener:

>=1.12.0,<1.13.0

depends bioconductor-qvalue:

>=2.38.0,<2.39.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:

>=3.20.0,<3.21.0

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

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-degcre

and update with::

   mamba update bioconductor-degcre

To create a new environment, run:

mamba create --name myenvname bioconductor-degcre

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-degcre:<tag>

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

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