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megadepth

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

megadepth: BigWig and BAM related utilities

Bioconductor version: Development (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")

# 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.

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 1.11.0
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
Linking To
Suggests covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat
System Requirements megadepth ()
Enhances
URL https://github.com/LieberInstitute/megadepth
Bug Reports https://support.bioconductor.org/t/megadepth
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package megadepth_1.11.0.tar.gz
Windows Binary megadepth_1.11.0.zip
macOS Binary (x86_64) megadepth_1.11.0.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