recipe bioconductor-segmenter

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/segmenter.html

License:

GPL-3

Recipe:

/bioconductor-segmenter/meta.yaml

Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.

package bioconductor-segmenter

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-bamsignals >=1.30.0,<1.31.0

• bioconductor-chipseeker >=1.34.0,<1.35.0

• bioconductor-chromhmmdata >=0.99.0,<0.100.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-segmenter

and update with:

conda update bioconductor-segmenter

or use the docker container:

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

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

Download stats

Link to this page

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