megadepth
This is thereleased version of megadepth; for the devel version, seemegadepth.
megadepth: BigWig and BAM related utilities
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-2140-308X, David Zhang [aut, cre] ORCID: 0000-0003-2382-8460
Maintainer: David Zhang <david.zhang.12 at ucl.ac.uk>
citation("megadepth")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("megadepth")For older versions of R, please refer to the appropriateBioconductor 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 | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (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 | chevreulProcess |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | megadepth_1.20.0.tar.gz |
| Windows Binary (x86_64) | megadepth_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | megadepth_1.20.0.tgz |
| macOS Binary (arm64) | megadepth_1.20.0.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 |