Introduction | An Example Workflow by Using Rbowtie2 | Installation | Loading | AdapterRemoval | Idetitify Adapter | Remove Adapter | Additional Arguments and Version | Bowtie2 | Build Bowtie2 Index | Additional Arguments of Bowtie Build | Bowtie2 Alignment | Additional Arguments and Version of Bowtie2 Aligner | Session Infomation | Acknowledgement | References
Package: Rbowtie2 2.19.0
Zheng Wei
Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval
This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.
Authors:
Rbowtie2_2.19.0.tar.gz
Rbowtie2_2.19.0.zip(r-4.7)Rbowtie2_2.19.0.zip(r-4.6)Rbowtie2_2.19.0.zip(r-4.5)
Rbowtie2_2.19.0.tgz(r-4.6-x86_64)Rbowtie2_2.19.0.tgz(r-4.6-arm64)Rbowtie2_2.19.0.tgz(r-4.5-x86_64)Rbowtie2_2.19.0.tgz(r-4.5-arm64)
Rbowtie2_2.19.0.tar.gz(r-4.7-arm64)Rbowtie2_2.19.0.tar.gz(r-4.7-x86_64)Rbowtie2_2.19.0.tar.gz(r-4.6-arm64)Rbowtie2_2.19.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rbowtie2/json (API)
| # Install 'Rbowtie2' in R: |
| install.packages('Rbowtie2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Rbowtie2-2.19.0(bioc 3.24)Rbowtie2-2.18.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingalignmentpreprocessingcpp
Last updated from:8a7676d920. Checks:5 NOTE, 7 WARNING, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 360 | ||
| linux-devel-arm64 | WARNING | 399 | ||
| linux-devel-x86_64 | WARNING | 388 | ||
| source / vignettes | OK | 633 | ||
| linux-release-arm64 | WARNING | 427 | ||
| linux-release-x86_64 | WARNING | 452 | ||
| macos-release-arm64 | NOTE | 208 | ||
| macos-release-x86_64 | NOTE | 578 | ||
| macos-oldrel-arm64 | NOTE | 245 | ||
| macos-oldrel-x86_64 | NOTE | 576 | ||
| windows-devel | WARNING | 345 | ||
| windows-release | WARNING | 345 | ||
| windows-oldrel | WARNING | 361 | ||
| wasm-release | FAIL | 351 |
Exports:adapterremoval_usageadapterremoval_versionbowtie2bowtie2_buildbowtie2_build_usagebowtie2_samtoolsbowtie2_usagebowtie2_versionidentify_adaptersremove_adapters
Dependencies:BHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayonformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rmagrittrRhtslibRsamtoolsS4VectorsSeqinfosnowXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Make system call for binaries | .callbinary |
| Print available arguments for adapterremoval | adapterremoval_usage |
| Print version information of adapterremoval | adapterremoval_version |
| Interface to bowtie2 of bowtie2-2.2.3 | bowtie2 |
| Print available arguments that can be passed to bowtie2_build() | bowtie2_build_usage |
| Interface to bowtie2-2.4.4 align function | bowtie2_samtools |
| Print available arguments that can be passed to bowtie2() | bowtie2_usage |
| Print version information of bowtie2-2.4.4 | bowtie2_version |
| Interface to bowtie2-2.4.4 build function | bowtie2-build bowtie2_build |
| Check if file is creatable | checkFileCreatable checkFileCreateable |
| Check if file exists | checkFileExist |
| Determine bowtie2 index type | checkIndexType |
| Check if path exists | checkPathExist |
| Check if samtools exists on the system | checkSamtoolsExists |
| identify adapters for paired-end reads | identify_adapters |
| Interface to bowtie2 of adapterremoval-2.2.1a | remove_adapters |
