- recipe bioconductor-hiannotator
Functions for annotating GRanges objects
GPL (>= 2)
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¶
- depends bioconductor-bsgenome:
- depends bioconductor-genomicranges:
- depends bioconductor-rtracklayer:
- depends r-base:
- depends r-dplyr:
- depends r-foreach:
- depends r-ggplot2:
- depends r-iterators:
- depends r-scales:
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
myenvnamebeing 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>``)