To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

hiAnnotator

 

   

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

Functions for annotating GRanges objects

Bioconductor version: Development (3.4)

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 and enter:

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

Documentation

HTML R Script Using hiAnnotator
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Software
Version 1.7.3
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL (>= 2)
Depends GenomicRanges, R (>= 2.10)
Imports foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales
LinkingTo
Suggests knitr, doParallel, testthat, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me hiReadsProcessor
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source hiAnnotator_1.7.3.tar.gz
Windows Binary hiAnnotator_1.7.3.zip
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/hiAnnotator
Package Short Url http://bioconductor.org/packages/hiAnnotator/
Package Downloads Report Download Stats

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