megadepth

DOI: 10.18129/B9.bioc.megadepth  

megadepth: BigWig and BAM related utilities

Bioconductor version: Release (3.17)

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

Author: Leonardo Collado-Torres [aut] , David Zhang [aut, cre]

Maintainer: David Zhang <david.zhang.12 at ucl.ac.uk>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("megadepth")

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("megadepth")

 

HTML	R Script	megadepth quick start guide
PDF		Reference Manual
Text		NEWS
Text		INSTALL

Details

biocViews	Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends
Imports	xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr
LinkingTo
Suggests	covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat
SystemRequirements	megadepth ()
Enhances
URL	https://github.com/LieberInstitute/megadepth
BugReports	https://support.bioconductor.org/t/megadepth
Depends On Me
Imports Me	dasper, ODER
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	megadepth_1.10.0.tar.gz
Windows Binary	megadepth_1.10.0.zip
macOS Binary (x86_64)	megadepth_1.10.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/megadepth
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/megadepth
Bioc Package Browser	https://code.bioconductor.org/browse/megadepth/
Package Short Url	https://bioconductor.org/packages/megadepth/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive