DOI: 10.18129/B9.bioc.metagene  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see metagene.

A package to produce metagene plots

Bioconductor version: 3.16

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")):


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HTML R Script Introduction to metagene
HTML R Script RNA-seq exp ext
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biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 2.30.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 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
Suggests BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown
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