Package: Rbowtie2 2.13.0

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:Zheng Wei [aut, cre], Wei Zhang [aut]

Rbowtie2_2.13.0.tar.gz

Rbowtie2_2.13.0.tgz(r-4.4-x86_64)Rbowtie2_2.13.0.tgz(r-4.4-arm64)Rbowtie2_2.13.0.tgz(r-4.3-x86_64)Rbowtie2_2.13.0.tgz(r-4.3-arm64)
Rbowtie2_2.13.0.tar.gz(r-4.5-noble)Rbowtie2_2.13.0.tar.gz(r-4.4-noble)
Rbowtie2.pdf |Rbowtie2.html✨
Rbowtie2/json (API)
NEWS

# Install 'Rbowtie2' in R:

install.packages('Rbowtie2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:Rbowtie2-2.13.0(bioc 3.21)Rbowtie2-2.12.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing alignment preprocessing

5.39 score 3 packages 27 scripts 638 downloads 10 exports 32 dependencies

Last updated 25 days agofrom:d83f9de809. Checks:OK: 1 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-mac-x86_64	NOTE	Oct 31 2024
R-4.4-mac-aarch64	NOTE	Oct 31 2024
R-4.3-mac-x86_64	NOTE	Oct 31 2024
R-4.3-mac-aarch64	NOTE	Oct 31 2024

Exports:adapterremoval_usage adapterremoval_version bowtie2 bowtie2_build bowtie2_build_usage bowtie2_samtools bowtie2_usage bowtie2_version identify_adapters remove_adapters

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r magrittr mime openssl R6 Rhtslib Rsamtools S4Vectors snow sys UCSC.utils XVector zlibbioc

An Introduction to Rbowtie2

Zheng Wei and Wei Zhang

Rendered fromRbowtie2-Introduction.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-09-18
Started: 2017-08-23

Citation

Development and contributors

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