recipe phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

Homepage:

https://github.com/kundajelab/phantompeakqualtools

License:

BSD-3-Clause

Recipe:

/phantompeakqualtools/meta.yaml

Links:

doi: 10.1101/gr.136184.111, doi: 10.1038/nbt.1508

package phantompeakqualtools

versions:

1.2.2-1,  1.2.2-0,  1.2.1.1-0,  1.2.1-0,  1.2-1,  1.2-0

depends bioconductor-rsamtools:

depends boost:

depends gawk:

depends r-base:

>=3.1

depends r-bitops:

depends r-catools:

depends r-snow:

depends r-snowfall:

depends r-spp:

>=1.13

depends samtools:

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 phantompeakqualtools

and update with::

   mamba update phantompeakqualtools

To create a new environment, run:

mamba create --name myenvname phantompeakqualtools

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/phantompeakqualtools:<tag>

(see `phantompeakqualtools/tags`_ for valid values for ``<tag>``)

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