Package: megadepth 1.23.0

David Zhang

megadepth: megadepth: BigWig and BAM related utilities

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.

Authors:Leonardo Collado-Torres [aut], David Zhang [aut, cre]

megadepth_1.23.0.tar.gz
megadepth_1.23.0.zip(r-4.7)megadepth_1.23.0.zip(r-4.6)megadepth_1.23.0.zip(r-4.5)
megadepth_1.23.0.tgz(r-4.6-any)megadepth_1.23.0.tgz(r-4.5-any)
megadepth_1.23.0.tar.gz(r-4.7-any)megadepth_1.23.0.tar.gz(r-4.6-any)
megadepth_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
megadepth/json (API)
NEWS

# Install 'megadepth' in R:

install.packages('megadepth', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lieberinstitute/megadepth/issues

On BioConductor:megadepth-1.23.0(bioc 3.24)megadepth-1.22.0(bioc 3.23)

software coverage dataimport transcriptomics rnaseq preprocessing bam bigwig daspter megadepth recount2 recount3

6.90 score 14 stars 3 packages 14 scripts 504 downloads 1 mentions 10 exports 67 dependencies

Last updated from:73f027de89. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	187
linux-devel-x86_64	OK	335
source / vignettes	OK	271
linux-release-x86_64	OK	316
macos-release-arm64	OK	202
macos-oldrel-arm64	OK	351
windows-devel	OK	177
windows-release	OK	156
windows-oldrel	OK	184
wasm-release	OK	174

Exports:bam_to_bigwig bam_to_junctions get_coverage install_megadepth megadepth_cmd megadepth_shell process_junction_table read_coverage read_coverage_table read_junction_table

Dependencies:askpass BiocGenerics bit bit64 brio callr cli clipr cmdfun cpp11 crayon credentials curl desc diffobj dplyr evaluate fs generics GenomicRanges gert gitcreds glue hms httr2 ini IRanges jsonlite lifecycle magrittr openssl pillar pkgbuild pkgconfig pkgload praise prettyunits processx progress ps purrr R.methodsS3 R.oo R.utils R6 rappdirs readr rlang rprojroot rstudioapi S4Vectors Seqinfo sys testthat tibble tidyselect tzdb usethis utf8 vctrs vroom waldo whisker withr xfun yaml zip

megadepth quick start guide

David Zhang, Leonardo Collado-Torres

Rendered frommegadepth.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-12-12
Started: 2020-09-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a BAM file to a BigWig	bam_to_bigwig
Extract junctions from a BAM file	bam_to_junctions
Compute coverage summarizations across a set of regions	get_coverage
Install Megadepth	install_megadepth
Run Megadepth commands	megadepth_cmd megadepth_shell
Process junctions into a STAR compatible format	process_junction_table
Read a coverage TSV file created by Megadepth	read_coverage read_coverage_table
Read a junction TSV file created by Megadepth as a table	read_junction_table