- recipe bioconductor-epiregulon
Gene regulatory network inference from single cell epigenomic data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/epiregulon.html
- License:
MIT + file LICENSE
- Recipe:
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¶
- versions:
1.2.0-0- depends bioconductor-annotationhub:
>=3.14.0,<3.15.0- depends bioconductor-annotationhub:
>=3.14.0,<3.15.0a0- depends bioconductor-assorthead:
>=1.0.0,<1.1.0- depends bioconductor-assorthead:
>=1.0.0,<1.1.0a0- depends bioconductor-aucell:
>=1.28.0,<1.29.0- depends bioconductor-aucell:
>=1.28.0,<1.29.0a0- depends bioconductor-beachmat:
>=2.22.0,<2.23.0- depends bioconductor-beachmat:
>=2.22.0,<2.23.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-bluster:
>=1.16.0,<1.17.0- depends bioconductor-bluster:
>=1.16.0,<1.17.0a0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.3,<1.5.0a0- depends bioconductor-bsgenome.hsapiens.ucsc.hg38:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg38:
>=1.4.5,<1.5.0a0- depends bioconductor-bsgenome.mmusculus.ucsc.mm10:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.mmusculus.ucsc.mm10:
>=1.4.3,<1.5.0a0- depends bioconductor-experimenthub:
>=2.14.0,<2.15.0- depends bioconductor-experimenthub:
>=2.14.0,<2.15.0a0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-motifmatchr:
>=1.28.0,<1.29.0- depends bioconductor-motifmatchr:
>=1.28.0,<1.29.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-scmultiome:
>=1.6.0,<1.7.0- depends bioconductor-scmultiome:
>=1.6.0,<1.7.0a0- depends bioconductor-scran:
>=1.34.0,<1.35.0- depends bioconductor-scran:
>=1.34.0,<1.35.0a0- depends bioconductor-scuttle:
>=1.16.0,<1.17.0- depends bioconductor-scuttle:
>=1.16.0,<1.17.0a0- depends bioconductor-singlecellexperiment:
>=1.28.0,<1.29.0- depends bioconductor-singlecellexperiment:
>=1.28.0,<1.29.0a0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx:
>=13- depends r-base:
>=4.4,<4.5.0a0- depends r-checkmate:
- depends r-entropy:
- depends r-lifecycle:
- depends r-matrix:
- depends r-rcpp:
- 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 and update with:: mamba update bioconductor-epiregulon
To create a new environment, run:
mamba create --name myenvname bioconductor-epiregulon
with
myenvnamebeing 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:<tag> (see `bioconductor-epiregulon/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-epiregulon/README.html)
