metagene
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Imetagene.
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 crchul.ulaval.ca>, Fabien Claude Lamaze <fabien.lamaze.1 at ulaval.ca>, Rawane Samb <rawane.samb.1 at ulaval.ca>, Cedric Lippens <lippens.cedric at protonmail>, Astrid Louise Deschenes <Astrid-Louise.Deschenes at crchudequebec.ulaval.ca> and Arnaud Droit <arnaud.droit at crchuq.ulaval.ca>.
Maintainer: Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>
citation("metagene")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("metagene")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
| Version | 2.36.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/CharlesJB/metagene/issues |
See More
| Suggests | BiocGenerics, similaRpeak, 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 | |
| Windows Binary (x86_64) | metagene_2.36.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/metagene |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagene |
| Package Short Url | https://bioconductor.org/packages/metagene/ |
| Package Downloads Report | Download Stats |