Package: megadepth 1.17.0

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]

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megadepth.pdf |megadepth.html✨
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-1.17.0(bioc 3.21)megadepth-1.16.0(bioc 3.20)

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

6.17 score 11 stars 1 packages 7 scripts 372 downloads 1 mentions 10 exports 76 dependencies

Last updated 9 days agofrom:d53868dfa8. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 14 2024
R-4.5-win	OK	Dec 14 2024
R-4.5-linux	OK	Dec 14 2024
R-4.4-win	OK	Dec 14 2024
R-4.4-mac	OK	Dec 14 2024
R-4.3-win	OK	Dec 14 2024
R-4.3-mac	OK	Dec 14 2024

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 digest dplyr evaluate fansi fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges gert gh gitcreds glue hms httr httr2 ini IRanges jsonlite lifecycle magrittr mime openssl pillar pkgbuild pkgconfig pkgload praise prettyunits processx progress ps purrr R.methodsS3 R.oo R.utils R6 rappdirs readr rlang rprojroot rstudioapi S4Vectors sys testthat tibble tidyselect tzdb UCSC.utils usethis utf8 vctrs vroom waldo whisker withr xfun XVector yaml zip zlibbioc

megadepth quick start guide

David Zhang, Leonardo Collado-Torres

Rendered frommegadepth.Rmdusingknitr::rmarkdownon Dec 14 2024.

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