recipe bioconductor-hiannotator

Functions for annotating GRanges objects

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/hiAnnotator.html

License:

GPL (>= 2)

Recipe:

/bioconductor-hiannotator/meta.yaml

Links:

biotools: hiannotator, doi: 10.1038/nmeth.3252

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.

package bioconductor-hiannotator

versions:

1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0, 

1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0,  1.14.0-0,  1.11.1-0

depends bioconductor-bsgenome:

>=1.74.0,<1.75.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-iterators:

depends r-scales:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-hiannotator

and update with::

   mamba update bioconductor-hiannotator

To create a new environment, run:

mamba create --name myenvname bioconductor-hiannotator

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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-hiannotator/README.html)