genomation

DOI: 10.18129/B9.bioc.genomation    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see genomation.

Summary, annotation and visualization of genomic data

Bioconductor version: 3.15

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb], Bozena Mika-Gospodorz [ctb]

Maintainer: Altuna Akalin <aakalin at gmail.com>, Vedran Franke <vedran.franke at gmail.com>, Katarzyna Wreczycka <katwre at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("genomation")

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("genomation")

 

HTML	R Script	genomation
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, CpGIsland, Sequencing, Software, Visualization
Version	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), grid
Imports	Biostrings(>= 2.47.6), BSgenome(>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges(>= 1.31.8), GenomicAlignments(>= 1.15.6), S4Vectors(>= 0.17.25), ggplot2, gridBase, impute, IRanges(>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools(>= 1.31.2), seqPattern, rtracklayer(>= 1.39.7), Rcpp (>= 0.12.14)
LinkingTo	Rcpp
Suggests	BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit
SystemRequirements
Enhances
URL	http://bioinformatics.mdc-berlin.de/genomation/
BugReports	https://github.com/BIMSBbioinfo/genomation/issues
Depends On Me
Imports Me	CexoR, EpiCompare, fCCAC, RCAS
Suggests Me	methylKit
Links To Me
Build Report

Package Archives

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

Source Package	genomation_1.28.0.tar.gz
Windows Binary	genomation_1.28.0.zip (64-bit only)
macOS Binary (x86_64)	genomation_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genomation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genomation
Package Short Url	https://bioconductor.org/packages/genomation/
Package Downloads Report	Download Stats