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genomation

Summary, annotation and visualization of genomic data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("genomation")):

Installation

To install this package, start R (version "4.3") 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")
genomation HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, CpGIsland, Sequencing, Software, Visualization
Version 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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)
System Requirements
URL http://bioinformatics.mdc-berlin.de/genomation/
Bug Reports https://github.com/BIMSBbioinfo/genomation/issues
See More
Suggests BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit
Linking To Rcpp
Enhances
Depends On Me
Imports Me CexoR, EpiCompare, fCCAC, GenomicPlot, RCAS
Suggests Me methylKit
Links To Me
Build Report Build Report

Package Archives

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

Source Package genomation_1.34.0.tar.gz
Windows Binary genomation_1.34.0.zip (64-bit only)
macOS Binary (x86_64) genomation_1.34.0.tgz
macOS Binary (arm64) genomation_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/genomation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genomation
Bioc Package Browser https://code.bioconductor.org/browse/genomation/
Package Short Url https://bioconductor.org/packages/genomation/
Package Downloads Report Download Stats