hiAnnotator

DOI: 10.18129/B9.bioc.hiAnnotator    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see hiAnnotator.

Functions for annotating GRanges objects

Bioconductor version: 3.7

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hiAnnotator")

Documentation

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

browseVignettes("hiAnnotator")

 

HTML	R Script	Using hiAnnotator
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Software
Version	1.14.0
In Bioconductor since	BioC 3.0 (R-3.1) (4 years)
License	GPL (>= 2)
Depends	GenomicRanges, R (>= 2.10)
Imports	foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods
LinkingTo
Suggests	knitr, doParallel, testthat, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me	hiReadsProcessor
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	hiAnnotator_1.14.0.tar.gz
Windows Binary	hiAnnotator_1.14.0.zip
Mac OS X 10.11 (El Capitan)	hiAnnotator_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/hiAnnotator
Source Repository (Developer Access)	git clone [email protected]:packages/hiAnnotator
Package Short Url	http://bioconductor.org/packages/hiAnnotator/
Package Downloads Report	Download Stats