recipe bioconductor-epiregulon.extra

Companion package to epiregulon with additional plotting, differential and graph functions

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/epiregulon.extra.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-epiregulon.extra/meta.yaml

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

package bioconductor-epiregulon.extra

versions:

1.2.0-0

depends bioconductor-clusterprofiler:

>=4.14.0,<4.15.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-scater:

>=1.34.0,<1.35.0

depends bioconductor-scran:

>=1.34.0,<1.35.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-checkmate:

depends r-circlize:

depends r-ggplot2:

depends r-ggraph:

depends r-igraph:

depends r-lifecycle:

depends r-matrix:

depends r-patchwork:

depends r-reshape2:

depends r-scales:

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-epiregulon.extra

and update with::

   mamba update bioconductor-epiregulon.extra

To create a new environment, run:

mamba create --name myenvname bioconductor-epiregulon.extra

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-epiregulon.extra:<tag>

(see `bioconductor-epiregulon.extra/tags`_ for valid values for ``<tag>``)

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