This is the development version of megadepth; for the stable release version, see megadepth.
megadepth: BigWig and BAM related utilitiesBioconductor version: Development (3.22)
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] ORCID: 0000-0003-2140-308X , David Zhang [aut, cre] ORCID: 0000-0003-2382-8460
Maintainer: David Zhang <david.zhang.12 at ucl.ac.uk>
Citation (from within R, entercitation("megadepth")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("megadepth")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("megadepth")Follow Installation instructions to use this package in your R session.
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