hiAnnotator
Functions for annotating GRanges objects
Bioconductor version: Release (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, Software |
| Version | 1.40.0 |
| 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_1.40.0.tar.gz |
| Windows Binary (x86_64) | hiAnnotator_1.40.0.zip |
| macOS Binary (x86_64) | hiAnnotator_1.40.0.tgz |
| macOS Binary (arm64) | hiAnnotator_1.40.0.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 |