recipe bioconductor-hiannotator

hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/hiAnnotator.html

License

GPL (>= 2)

Recipe

/bioconductor-hiannotator/meta.yaml

Links

biotools: hiannotator, doi: 10.1038/nmeth.3252

package bioconductor-hiannotator

Versions

1.16.0-0, 1.14.0-0, 1.11.1-0

Depends

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• r-base >=3.5.1,<3.5.2.0a0

• r-dplyr

• r-foreach

• r-ggplot2

• r-iterators

• r-scales

Required By

• bioconductor-hireadsprocessor

Installation

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

conda install bioconductor-hiannotator

and update with:

conda update bioconductor-hiannotator

or use the docker container:

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

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

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-hiannotator/README.html)