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Functions for annotating GRanges objects.

Bioconductor version: 3.0

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>

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biocViews Annotation, Software
Version 1.0.0
In Bioconductor since BioC 3.0 (R-3.1)
License GPL (>= 2)
Depends GenomicRanges, R (>= 2.10)
Imports foreach, iterators, rtracklayer, plyr, BSgenome, ggplot2, scales
Suggests knitr, doParallel, testthat, BiocGenerics
Depends On Me hiReadsProcessor
Imports Me
Suggests Me
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Package Source hiAnnotator_1.0.0.tar.gz
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