Decoding herpes simplex virus 1 by integrative multi-omics
Creators
- Whisnant, Adam1
- Jürges, Christopher1
- Hennig, Thomas1
- Wyler, Emanuel2
- Prusty, Bhupesh1
- L'hernault, Anne3
- Göbel, Margarete4
- Döring, Kristina4
- Menegatti, Jennifer5
- Rufkowski, Andrzej3
- Matheson, Nick6
- Künzig Florian1
- Mastrobuino, Guido2
- Bielow, Chris2
- Kempa, Stefan2
- Chunguang, Liang7
- Dandekar, Thomas7
- Zimmer, Ralf8
- Landthaler, Markus2
- Grässer, Friedrich5
- Lehner, Paul6
- Friedel, Caroline8
- Erhard, Florian1
- Dölken, Lars1
- 1. Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg
- 2. Berlin Institute for Medical Systems Biology
- 3. Department of Medicine, University of Cambridge
- 4. Core Unit Systems Medicine, Julius-Maximilians-University Würzburg
- 5. Institute of Virology, Saarland University Medical School Homburg/Saar
- 6. Department of Medicine, Cambridge Institute for Medical Research
- 7. Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians-University Würzburg
- 8. Institute of Informatics, Ludwig-Maximilians-Universität München
Description
Here, two folders are provided. The one titled "figures_and_tables" contains the scripts for creating the figures and tables of our paper (except for the ones containing only screenshots of i.e. blots). The one titles "iTiSS_program" contains the program iTiss and instructions on how to run it on the provided dataset to replicate our findings of our paper.
Both folders contain a README with instructions on how to execute the scripts and their requirements. In short, figures_and_tables contains a makefile, which can be run by simply calling 'make'. iTiSS_program contains a make.bash, which needs to be executed to run everything.
In general, however, all figures are already created and exist inside the folders. Only if you want to RErun everything you should be executing the makefile, and make.bash.
System requirements:
Java 1.8, R (including the following libraries: lfc, scales, ggplot2, ggforce, reshape2, plyr, cowplot, ggrepel, circlize, RWebLogo, complexHeatmap, gird, gridExtra)