- 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:
- License:
BSD-3-Clause
- Recipe:
- 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:
on bioconductor-rsamtools
on boost
on gawk
on r-base
>=3.1on r-bitops
on r-catools
on r-snow
on r-snowfall
on r-spp
>=1.13on samtools
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install phantompeakqualtools
to add into an existing workspace instead, run:
pixi add phantompeakqualtools
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install phantompeakqualtools
Alternatively, to install into a new environment, run:
conda create -n envname phantompeakqualtools
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/phantompeakqualtools:<tag>
(see phantompeakqualtools/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/phantompeakqualtools/README.html)
