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:
megadepth_1.17.0.tar.gz
megadepth_1.17.0.zip(r-4.5)megadepth_1.17.0.zip(r-4.4)megadepth_1.17.0.zip(r-4.3)
megadepth_1.17.0.tgz(r-4.4-any)megadepth_1.17.0.tgz(r-4.3-any)
megadepth_1.17.0.tar.gz(r-4.5-noble)megadepth_1.17.0.tar.gz(r-4.4-noble)
megadepth_1.17.0.tgz(r-4.4-emscripten)megadepth_1.17.0.tgz(r-4.3-emscripten)
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-1.15.0(bioc 3.20)megadepth-1.14.0(bioc 3.19)
softwarecoveragedataimporttranscriptomicsrnaseqpreprocessingbambigwigdasptermegadepthrecount2recount3
Last updated 22 days agofrom:019b9f01d7. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:bam_to_bigwigbam_to_junctionsget_coverageinstall_megadepthmegadepth_cmdmegadepth_shellprocess_junction_tableread_coverageread_coverage_tableread_junction_table
Dependencies:askpassBiocGenericsbitbit64briocallrclicliprcmdfuncpp11crayoncredentialscurldescdiffobjdigestdplyrevaluatefansifsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgertghgitcredsgluehmshttrhttr2iniIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrematch2rlangrprojrootrstudioapiS4VectorssystestthattibbletidyselecttzdbUCSC.utilsusethisutf8vctrsvroomwaldowhiskerwithrxfunXVectoryamlzipzlibbioc
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 |
