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megadepth

megadepth: BigWig and BAM related utilities


Bioconductor version: Release (3.18)

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")):

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

Details

biocViews Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends
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
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package megadepth_1.12.0.tar.gz
Windows Binary megadepth_1.12.0.zip (64-bit only)
macOS Binary (x86_64) megadepth_1.12.0.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