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:
megadepth_1.23.0.tar.gz
megadepth_1.23.0.zip(r-4.7-any)megadepth_1.23.0.zip(r-4.6-any)megadepth_1.23.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
megadepth/json (API)
| # 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)
softwarecoveragedataimporttranscriptomicsrnaseqpreprocessingbambigwigdasptermegadepthrecount2recount3
Last updated from:73f027de89. Checks:4 WARNING, 5 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 169 | ||
| linux-devel | ERROR | 267 | ||
| source / vignettes | ERROR | 270 | ||
| linux-release | ERROR | 284 | ||
| macos-release | ERROR | 168 | ||
| macos-oldrel | ERROR | 157 | ||
| windows-devel | WARNING | 147 | ||
| windows-release | WARNING | 153 | ||
| windows-oldrel | WARNING | 156 | ||
| wasm-release | OK | 156 |
Exports:bam_to_bigwigbam_to_junctionsget_coverageinstall_megadepthmegadepth_cmdmegadepth_shellprocess_junction_tableread_coverageread_coverage_tableread_junction_table
Dependencies:askpassBiocGenericsbitbit64briocallrclicliprcmdfuncpp11crayoncredentialscurldescdiffobjdplyrevaluatefsgenericsGenomicRangesgertgitcredsgluehmshttr2iniIRangesjsonlitelifecyclemagrittropensslotelpakpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrlangrprojrootrstudioapiS4VectorsSeqinfosystestthattibbletidyselecttzdbusethisutf8vctrsvroomwaldowhiskerwithrxfunyamlzip
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 |