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This is the development version of hiAnnotator; for the stable release version, see hiAnnotator.

Functions for annotating GRanges objects

Bioconductor version: Development (3.20)

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.

Author: Nirav V Malani <malnirav at>

Maintainer: Nirav V Malani <malnirav at>

Citation (from within R, enter citation("hiAnnotator")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using hiAnnotator HTML R Script
Reference Manual PDF


biocViews Annotation, Software
Version 1.39.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL (>= 2)
Depends GenomicRanges, R (>= 2.10)
Imports foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods
System Requirements
See More
Suggests knitr, doParallel, testthat, BiocGenerics, markdown
Linking To
Depends On Me hiReadsProcessor
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package hiAnnotator_1.39.0.tar.gz
Windows Binary
macOS Binary (x86_64) hiAnnotator_1.39.0.tgz
macOS Binary (arm64) hiAnnotator_1.39.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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