Package Recipe 'bioconductor-nupop'

recipe bioconductor-nupop

An R package for nucleosome positioning prediction

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/NuPoP.html
License:: GPL-2
Recipe:: /bioconductor-nupop/meta.yaml

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.

package bioconductor-nupop¶

Versions:

2.18.0-0, 2.14.0-0, 2.10.0-1, 2.10.0-0, 2.8.1-0, 2.6.0-1, 2.6.0-0, 2.2.0-2, 2.2.0-1,

2.18.0-0, 2.14.0-0, 2.10.0-1, 2.10.0-0, 2.8.1-0, 2.6.0-1, 2.6.0-0, 2.2.0-2, 2.2.0-1, 2.2.0-0, 2.0.0-0, 1.40.0-1, 1.40.0-0, 1.38.0-0, 1.36.0-0, 1.34.0-2, 1.34.0-1, 1.34.0-0, 1.32.0-0

Depends:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on libgfortran
on libgfortran5 >=14.3.0
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0

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 bioconductor-nupop

to add into an existing workspace instead, run:

pixi add bioconductor-nupop

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 bioconductor-nupop

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nupop

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/bioconductor-nupop:<tag>

(see bioconductor-nupop/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-nupop/README.html)