Package Recipe 'bioconductor-nearbynding'

recipe bioconductor-nearbynding

Discern RNA structure proximal to protein binding

Homepage:: https://bioconductor.org/packages/3.20/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:

1.16.0-0, 1.12.0-0, 1.10.0-0, 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:

on bioconductor-biocgenerics >=0.52.0,<0.53.0
on bioconductor-genomeinfodb >=1.42.0,<1.43.0
on bioconductor-genomicranges >=1.58.0,<1.59.0
on bioconductor-plyranges >=1.26.0,<1.27.0
on bioconductor-rsamtools >=2.22.0,<2.23.0
on bioconductor-rtracklayer >=1.66.0,<1.67.0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0
on r-base >=4.4,<4.5.0a0
on r-dplyr
on r-ggplot2
on r-gplots
on r-magrittr
on r-matrixstats
on r-r.utils
on r-rlang
on r-transport

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-nearbynding

to add into an existing workspace instead, run:

pixi add bioconductor-nearbynding

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-nearbynding

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nearbynding

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-nearbynding/README.html)