@@ -8,7 +8,11 @@ Thank you for the interest in diffTF! If you have questions or comments, feel fr
Summary
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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
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](https://www.biorxiv.org/content/early/2018/07/13/368498).
Documentation
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Changelog
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Version 1.0.1 (2018-07-25)
- fixed a bug in 2.DiffPeaks.R that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
Version 1.0 (2018-07-01)
- released stable version
[See the Documentation for a detailed changelog](http://difftf.readthedocs.io/en/latest/projectInfo.html#change-log)
Citation
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*Please cite the following article if you use diffTF in your research*:
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Rassmussen & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.
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. *Molecular Systems Biology*. in review.
If you use this software, please cite the following reference:
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
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. *Molecular Systems Biology*. in review.
We also put the paper on *bioRxiv*, please read all methodological details here:
`Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF <https://www.biorxiv.org/content/early/2018/07/13/368498>`_.
