README.md

Genome-wide quantification of differential transcription factor activity: diffTF

Thank you for the interest in diffTF! If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation.

Summary

Transcription factor (TF) activity constitutes an important readout of cellular signalling pathways and thus for assessing regulatory differences across conditions. However, current technologies lack the ability to simultaneously assessing activity changes for multiple TFs and surprisingly little is known about whether a TF acts as repressor or activator. To this end, we introduce the widely applicable genome-wide method diffTF to assess differential TF binding activity and classifying TFs as activator or repressor by integrating any type of genome-wide chromatin with RNA-Seq data and in-silico predicted TF binding sites.

For more information, please check our paper on biorxiv:

Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF.

Documentation

A detailed Documentation is available here

Installation and Quick Start

Please see the Documentation for easy "Installation and Quick Start" instructions.

Changelog

See the Documentation for a detailed changelog

Citation

Please cite the following article if you use diffTF in your research:

Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Giovanni Palla, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF. 2018. in review.