megadepth

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see megadepth.

megadepth: BigWig and BAM related utilities

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics

Version 1.8.0

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

Suggests covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat

Linking To

Enhances

Depends On Me

Imports Me dasper, ODER

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package megadepth_1.8.0.tar.gz

Windows Binary megadepth_1.8.0.zip (64-bit only)

macOS Binary (x86_64) megadepth_1.8.0.tgz

macOS Binary (arm64) megadepth_1.8.0.tgz

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 3.16 Source Archive