recipe bioconductor-epimix

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/EpiMix.html

License:

GPL-3

Recipe:

/bioconductor-epimix/meta.yaml

EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.

package bioconductor-epimix

versions:

1.4.0-0,  1.1.2-0,  0.99.16-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-elmer.data:

>=2.26.0,<2.27.0

depends bioconductor-epimix.data:

>=1.4.0,<1.5.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-impute:

>=1.76.0,<1.77.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-dosnow:

depends r-downloader:

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-plyr:

depends r-progress:

depends r-r.matlab:

depends r-rcolorbrewer:

depends r-rcurl:

depends r-rlang:

depends r-rpmm:

depends r-tibble:

depends r-tidyr:

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-epimix

and update with::

   mamba update bioconductor-epimix

To create a new environment, run:

mamba create --name myenvname bioconductor-epimix

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-epimix:<tag>

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

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