Commit cc50e08d authored by Christian Arnold's avatar Christian Arnold

Referenced the bioRxiv paper in the Documentation

parent 91811391
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Workflow
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We 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>`_.
The workflow and conceptual idea behind *diffTF* is illustrated by the following three Figures. First, we give a high-level conceptual overview and a biological motivation:
.. figure:: Figures/diffTF_Schematic.png
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......@@ -6,6 +6,9 @@ Transcription factor (TF) activity constitutes an important readout of cellular
For a graphical summary of the idea, see the section :ref:`workflow`
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>`_.
Help, contribute and contact
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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. 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. 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>`_.
Change log
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Version 1.1 (2018-07-27)
- updated the TFBS files that are available via download (some files were not presorted correctly)
- added a new parameter *dir_TFBS_sorted* in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- added support for single-end BAM files. There is a new parameter *pairedEnd" in the config file now that specifies whether reads are paired-end or not.
- updated the TFBS files that are available via download (some files were not presorted correctly)
- added support for single-end BAM files. There is a new parameter *pairedEnd* in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule *concatenateMotifsPerm* should now be much faster, and the TF-specific *...outputPerm.tsv.gz* files are now much smaller due to an improved column structure
Version 1.0.1 (2018-07-25)
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