recipe bioconductor-nucpos

An R package for prediction of nucleosome positions






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


1.6.0-0, 1.4.0-0, 1.2.0-2, 1.2.0-1, 1.2.0-0, 1.0.1-0, 1.0.0-0

Required By


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<tag>

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