recipe bioconductor-nearbynding

Discern RNA structure proximal to protein binding

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-nearbynding/meta.yaml

Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.

package bioconductor-nearbynding

Versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-3,  1.0.0-2,  1.0.0-1

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-plyranges >=1.18.0,<1.19.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.16.0,<3.17.0

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-ggplot2

• r-gplots

• r-magrittr

• r-matrixstats

• r-r.utils

• r-rlang

• r-transport

Required By:

Installation

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

conda install bioconductor-nearbynding

and update with:

conda update bioconductor-nearbynding

or use the docker container:

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

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

Download stats

Link to this page

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