# 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.](https://bedtools.readthedocs.io/en/latest/content/installation.html) Installation instructions will vary by operating system. #### CapR Download the zip file from the [github repository](https://github.com/fukunagatsu/CapR), 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](https://github.com/favorov/stereogene), 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.