The Mathematica code underlying the analysis of a published scientific paper is hosted here in the interests of reproducibility.
Crocker, Ilsley and Stern. Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nature Genetics (2016). http://dx.doi.org/10.1038/ng.3509
The code requires Mathematica 10 and has been tested on 10.3.1.
The top-level directory contains the Mathematica script files, which can be run from the command line, for example:
math -script qTALEManuscriptFigures_eve.wl
The project has the following directory structure:
| Directory | Content |
|---|---|
| data | The rhomboid wild-type and TALE data underlying Figure 3 in the paper. |
| externalData | The data kindly supplied by D. Papatsenko and H. Janssens. |
| Figures | The figures generated by the Mathematica script files, with the subdirectories corresponding to the figures of the published paper. |
| packages | Mathematica package files used by the script files. The BDTNP.wl package file includes public data from the Berkeley Drosophila Transcription Network Project. The code to generate this package can be found at https://github.com/ilsley/wlBDTNP. |