megadepth

DOI: 10.18129/B9.bioc.megadepth    

megadepth: BigWig and BAM related utilities

Bioconductor version: Release (3.12)

This package provides an R interface to Megadepth by Christopher Wilks available at (). 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 .

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 "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics
Version 1.0.1
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Artistic-2.0
Depends
Imports xfun, utils, fs, GenomicRanges, readr, cmdfun
LinkingTo
Suggests covr, knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat
SystemRequirements megadepth ()
Enhances
URL https://github.com/LieberInstitute/megadepth
BugReports https://support.bioconductor.org/t/megadepth
Depends On Me
Imports Me dasper
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package megadepth_1.0.1.tar.gz
Windows Binary megadepth_1.0.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) megadepth_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/megadepth
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/megadepth
Package Short Url https://bioconductor.org/packages/megadepth/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive

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