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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see genomation.

Summary, annotation and visualization of genomic data

Bioconductor version: 3.4

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]

Maintainer: Altuna Akalin <aakalin at>, Vedran Franke <vedran.franke at>

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


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biocViews Annotation, CpGIsland, Sequencing, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.1 (R-3.2) (2 years)
License Artistic-2.0
Depends R (>= 3.0.0), grid
Imports Biostrings, BSgenome, data.table, GenomeInfoDb, GenomicRanges(>= 1.23.26), GenomicAlignments, S4Vectors(>= 0.9.25), ggplot2, gridBase, impute, IRanges, matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools, seqPattern, rtracklayer, Rcpp, RUnit
LinkingTo Rcpp, Rhtslib
Suggests BiocGenerics, genomationData, knitr, knitrBootstrap, RColorBrewer, rmarkdown
Depends On Me
Imports Me CexoR, fCCAC, RCAS
Suggests Me methylKit
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