DOI: 10.18129/B9.bioc.genomation    

Summary, annotation and visualization of genomic data

Bioconductor version: Release (3.6)

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>, Vedran Franke <vedran.franke at>, Katarzyna Wreczycka <katwre at>

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biocViews Annotation, CpGIsland, Sequencing, Software, Visualization
Version 1.11.3
In Bioconductor since BioC 3.1 (R-3.2) (3 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(>= 1.25.2), seqPattern, rtracklayer, RUnit, Rcpp (>= 0.12.14)
LinkingTo Rcpp
Suggests BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown
Depends On Me
Imports Me CexoR, fCCAC, RCAS
Suggests Me methylKit
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