Introduction | Preliminaries | Citing Rbowtie | Installation | Loading of Rbowtie | How to get help | Example usage for individual Rbowtie functions | Build the reference index with bowtie_build | Create alignment with bowtie | Create spliced alignment with SpliceMap | Session information | References
Package: Rbowtie 1.52.0
Michael Stadler
Rbowtie: R bowtie wrapper
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
Authors:
Rbowtie_1.52.0.tar.gz
Rbowtie_1.52.0.zip(r-4.7)Rbowtie_1.52.0.zip(r-4.6)Rbowtie_1.52.0.zip(r-4.5)
Rbowtie_1.52.0.tgz(r-4.6-x86_64)Rbowtie_1.52.0.tgz(r-4.6-arm64)Rbowtie_1.52.0.tgz(r-4.5-x86_64)Rbowtie_1.52.0.tgz(r-4.5-arm64)
Rbowtie_1.52.0.tar.gz(r-4.7-arm64)Rbowtie_1.52.0.tar.gz(r-4.7-x86_64)Rbowtie_1.52.0.tar.gz(r-4.6-arm64)Rbowtie_1.52.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rbowtie/json (API)
| # Install 'Rbowtie' in R: |
| install.packages('Rbowtie', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmicompbio/rbowtie/issues
On BioConductor:Rbowtie-1.53.0(bioc 3.24)Rbowtie-1.52.0(bioc 3.23)
Last updated from:890c9d501a (on RELEASE_3_23). Checks:7 WARNING, 5 NOTE, 1 OK, 1 FAIL. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 192 | ||
| linux-devel-arm64 | NOTE | 177 | ||
| linux-devel-x86_64 | NOTE | 205 | ||
| source / vignettes | OK | 303 | ||
| linux-release-arm64 | WARNING | 240 | ||
| linux-release-x86_64 | WARNING | 256 | ||
| macos-release-arm64 | WARNING | 104 | ||
| macos-release-x86_64 | WARNING | 362 | ||
| macos-oldrel-arm64 | WARNING | 101 | ||
| macos-oldrel-x86_64 | WARNING | 336 | ||
| windows-devel | NOTE | 166 | ||
| windows-release | NOTE | 237 | ||
| windows-oldrel | NOTE | 182 | ||
| wasm-release | FAIL | 107 |
Exports:bowtiebowtie_buildbowtie_build_usagebowtie_usagebowtie_versionSpliceMap
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| R bowtie wrapper | Rbowtie-package Rbowtie |
| Interface to bowtie | bowtie bowtie_build bowtie_build_usage bowtie_usage bowtie_version |
| Interface to SpliceMap | SpliceMap |
