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This is the development version of megadepth; for the stable release version, see megadepth.

megadepth: BigWig and BAM related utilities

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("megadepth")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

megadepth quick start guide HTML R Script
Reference Manual PDF


biocViews Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Imports xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr
System Requirements megadepth ()
URL https://github.com/LieberInstitute/megadepth
Bug Reports https://support.bioconductor.org/t/megadepth
See More
Suggests covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat
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Package Archives

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

Source Package megadepth_1.13.0.tar.gz
Windows Binary megadepth_1.13.0.zip
macOS Binary (x86_64) megadepth_1.13.0.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/
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