metagene2
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see metagene2.
A package to produce metagene plots
Bioconductor version: 3.9
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.
Author: Eric Fournier [cre, aut], Charles Joly Beauparlant [aut], Cedric Lippens [aut], Arnaud Droit [aut]
Maintainer: Eric Fournier <fournier.eric.2 at crchudequebec.ulaval.ca>
citation("metagene2")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("metagene2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagene2")| Introduction to metagene2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel |
| Imports | rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, DBChIP, purrr, data.table, methods, dplyr, magrittr |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ArnaudDroitLab/metagene2/issues |
See More
| Suggests | BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metagene2_1.0.0.tar.gz |
| Windows Binary | metagene2_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | metagene2_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/metagene2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagene2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/metagene2/ |
| Package Short Url | https://bioconductor.org/packages/metagene2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |