hiAnnotator

Functions for annotating GRanges objects


Bioconductor version: Release (3.19)

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 gmail.com>

Maintainer: Nirav V Malani <malnirav at gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("hiAnnotator")

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

Documentation

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

browseVignettes("hiAnnotator")
Using hiAnnotator HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Software
Version 1.38.0
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
URL
See More
Suggests knitr, doParallel, testthat, BiocGenerics, markdown
Linking To
Enhances
Depends On Me hiReadsProcessor
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package hiAnnotator_1.38.0.tar.gz
Windows Binary (x86_64) hiAnnotator_1.38.0.zip
macOS Binary (x86_64) hiAnnotator_1.38.0.tgz
macOS Binary (arm64) hiAnnotator_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hiAnnotator
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hiAnnotator
Bioc Package Browser https://code.bioconductor.org/browse/hiAnnotator/
Package Short Url https://bioconductor.org/packages/hiAnnotator/
Package Downloads Report Download Stats