recipe bioconductor-rbowtie2

An R Wrapper for Bowtie2 and AdapterRemoval

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/Rbowtie2.html

License:

GPL (>= 3)

Recipe:

/bioconductor-rbowtie2/meta.yaml

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.

package bioconductor-rbowtie2

Versions:

2.4.0-0,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

2.4.0-0,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0

Depends:

• bioconductor-rsamtools >=2.14.0,<2.15.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• libzlib >=1.2.13,<1.3.0a0

• r-base >=4.2,<4.3.0a0

• r-magrittr

• zlib >=1.2.13,<1.3.0a0

Required By:

• bioconductor-circseqaligntk

• bioconductor-umi4cats

• bioconductor-esatac

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-rbowtie2

and update with:

conda update bioconductor-rbowtie2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-rbowtie2:<tag>

(see bioconductor-rbowtie2/tags for valid values for <tag>)

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