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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

A package to produce metagene plots

Bioconductor version: Release (3.19)

This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.

Author: Charles Joly Beauparlant <charles.joly-beauparlant at>, Fabien Claude Lamaze <fabien.lamaze.1 at>, Rawane Samb <rawane.samb.1 at>, Cedric Lippens <lippens.cedric at protonmail>, Astrid Louise Deschenes <Astrid-Louise.Deschenes at> and Arnaud Droit <arnaud.droit at>.

Maintainer: Charles Joly Beauparlant <charles.joly-beauparlant at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 2.36.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, Rsamtools, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr
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Suggests BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown
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