metagene2
A package to produce metagene plots
Bioconductor version: 3.23 · Package version: 1.28.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("metagene2")Details
| Maintainer | Eric Fournier <ericfournier2@yahoo.ca> |
| Author | Eric Fournier [cre, aut], Charles Joly Beauparlant [aut], Cedric Lippens [aut], Arnaud Droit [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/ArnaudDroitLab/metagene2 |
| Bug Reports | https://github.com/ArnaudDroitLab/metagene2/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/metagene2/ |
Citation
From within R, enter citation("metagene2"):
Eric Fournier, Charles Joly Beauparlant, Cedric Lippens, Arnaud Droit. metagene2: A package to produce metagene plots. doi:10.18129/B9.bioc.metagene2, R package version 1.28.0, https://bioconductor.org/packages/metagene2.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | metagene2_1.28.0.tar.gz |
| Windows binary (x86_64) | metagene2_1.28.0.zip |
| macOS binary (arm64) | metagene2_1.28.0.tgz |
| macOS binary (x86_64) | metagene2_1.28.0.tgz |
Dependencies
Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2
Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown