DOI: 10.18129/B9.bioc.hiAnnotator    

Functions for annotating GRanges objects

Bioconductor version: Release (3.6)

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")):


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biocViews Annotation, Software
Version 1.12.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License GPL (>= 2)
Depends GenomicRanges, R (>= 2.10)
Imports foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods
Suggests knitr, doParallel, testthat, BiocGenerics
Depends On Me hiReadsProcessor
Imports Me
Suggests Me
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Source Package hiAnnotator_1.12.0.tar.gz
Windows Binary hiAnnotator_1.12.0.zip
Mac OS X 10.11 (El Capitan) hiAnnotator_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hiAnnotator
Package Short Url http://bioconductor.org/packages/hiAnnotator/
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