recipe bioconductor-nucpos

An R package for prediction of nucleosome positions

Homepage

https://bioconductor.org/packages/3.11/bioc/html/nuCpos.html

License

file LICENSE

Recipe

/bioconductor-nucpos/meta.yaml

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. In nuCpos, a duration hidden Markov model is trained with a chemical map of nucleosomes either from budding yeast, fission yeast, or mouse embryonic stem cells. nuCpos outputs the Viterbi (most probable) path of nucleosome-linker states, predicted nucleosome occupancy scores and histone binding affinity (HBA) scores as NuPoP does. nuCpos can also calculate local and whole nucleosomal HBA scores for a given 147-bp sequence. Furthermore, effect of genetic alterations on nucleosome occupancy can be predicted with this package. The parental package NuPoP, which is based on an MNase-seq-based map of budding yeast nucleosomes, was developed by Ji-Ping Wang and Liqun Xi, licensed under GPL-2.

package bioconductor-nucpos

(downloads) docker_bioconductor-nucpos

Versions

1.6.0-01.4.0-01.2.0-21.2.0-11.2.0-01.0.1-01.0.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-nucpos

and update with:

conda update bioconductor-nucpos

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-nucpos:<tag>

(see bioconductor-nucpos/tags for valid values for <tag>)