recipe atactk

A toolkit for working with ATAC-seq data.



GPL / GPL-3.0-or-later



package atactk

(downloads) docker_atactk



depends pysam:


depends python:

depends python-levenshtein:

depends r-base:

depends r-ggplot2:

depends r-gtools:

depends r-rcolorbrewer:

depends sexpdata:



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 atactk

and update with::

   mamba update atactk

To create a new environment, run:

mamba create --name myenvname atactk

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 `atactk/tags`_ for valid values for ``<tag>``)


Adds 3 scripts, namely "trim_adapters", "make_cut_matrix" and "plot_aggregate_matrix.R"

Download stats