nearBynding

nearBynding is an R package that discerns RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. Input CLIP protein-binding data can either be in aligned BAM or peak-called BED/bedGraph formats. RNA structure can either be internally calculated via CapR or can be provided by the user as a BED/bedGraph. RNA structure binding profiles can be visually and mathematically compared between proteins across multiple formats.

Installation

The most up-to-date version can be loaded to R via

devtools::install_github("vbusa1/nearBynding")
library(nearBynding)

External Software Dependencies

nearBynding requires three external softwares. Add all dependency directories to your PATH after installation.

bedtools

bedtools is available for installation here.

Installation instructions will vary by operating system.

CapR

Download the zip file from the github repository, unzip the file, and move it to a directory where you want to permanently store the function.

In the command line, access the folder where the unzipped file is stored.

cd CapR-master
make
./CapR

If installation is successful, the final line will output

Error: The number of argument is invalid.

StereoGene

Download the zip file from the github repository, unzip the file, and move it to a directory where you want to permanently store the function.

In the command line, access the folder where the unzipped file is stored.

cd stereogene-master
cd src
make
./stereogene -h

If installation is successful, the final line will output a menu of argument options.