megadepth
megadepth: BigWig and BAM related utilities
Bioconductor version: Release (3.20)
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("megadepth")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| INSTALL | Text |
Details
| biocViews | Coverage, DataImport, Preprocessing, RNASeq, Software, Transcriptomics |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 | |
| 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | megadepth_1.16.0.zip |
| macOS Binary (x86_64) | megadepth_1.16.0.tgz |
| macOS Binary (arm64) | megadepth_1.16.0.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 |