bindcompare 0.6.0

A Novel DNA/RNA Binding Integration and Analysis Platform.

BindCompare: A novel integrated protein-binding analysis platform

Introduction | Installation Guide | Using BindCompare | Quick Start | Credits

BindCompare Function Manuals: bindcompare | bindexplore | Downstream & comparexp

Introduction

BindCompare is a novel integrated protein-binding analysis platform designed to be user-accessible and interpretable. Given protein-binding sites on DNA and/or RNA, BindCompare determines and visualizes domains of co-regulatory activity at the single-nucleotide level.

At the core of BindCompare is defining overlapping binding domains. Oftentimes, co-regulation with factors occurs across a larger locus surrounding the marked binding site. BindCompare searches and categorizes overlaps across a scoped regions containing the reference binding sites. Because BindCompare utilizes BED files, it enables the comparison between RNA and DNA binding sites, aiding the study of system wide co-transcriptional regulation.

To support user-accessible software, BindCompare can be launched in a GUI interface that allows for easy application of bindcompare and comparexp. To learn how to utilize the tool, please read below and do not hesitate to reach out if any bugs or issues are revealed.

Quick Start

Install bindcompare and its dependencies from PyPI using pip:

pip install bindcompare

Then, to run the core function bindcompare:

bindcompare <ref bed> <exp bed> <scope: int> <sample name> <output dir> <GTF|None> <FA|None>

Alternatively, to launch the core GUI application, see below. For a more detailed walk-through, read the full documentation below and function specific manuals. Complete installation instructions can also be found at

Using BindCompare

Here is a general overview of BindCompare usage in the following schematic.

To start, optionally run bindexplore to find candidate co-regulators. Then, you can choose two candidate coregulators and run bindcompare to explore co-regulatory activities between the protein-binding datasets given. Finally, you can look into downstream analysis using comparexp or gene ontology/motif analysis.

As aforementioned, bindcompare and comparexp can be run through a tkinter GUI interface. All of the commands can be run from the command line. This includes retrievedm6 and bindexplore. How to use BindCompare is presented for both the GUI and command line approaches. To launch the GUI:

bindlaunch

That should launch a platform that looks like this:

Please visit the command specific pages for each of the above commands to learn more about how to use BindCompare.

Credits

This script was written at Brown University in the Larschan Lab by Pranav Mahableshwarkar under the guidance of Mukulika Ray, PhD and Erica Larschan, PhD.

If you want to pull the source-code, this can be done via github.

git pull https://github.com/pranavmahabs/bindcompare.git

Please leave any messages here regarding errors or issues found in using the platform.