megadepth
This is the released version of megadepth; for the devel version, see megadepth.
megadepth: BigWig and BAM related utilities
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, OleÅ AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115â121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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
Follow Installation instructions to use this package in your R session.
| Source Package | megadepth_1.22.0.tar.gz |
| Windows Binary (x86_64) | megadepth_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | megadepth_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | megadepth_1.22.0.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 |