recipe bioconductor-epistack

Heatmaps of Stack Profiles from Epigenetic Signals






The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.

package bioconductor-epistack

(downloads) docker_bioconductor-epistack



depends bioconductor-biocgenerics:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-plotrix:



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-epistack

and update with::

   mamba update bioconductor-epistack

To create a new environment, run:

mamba create --name myenvname bioconductor-epistack

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<tag>

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

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