This repository is a collection of source code that supported the analyses of the NLR gene family in hexaploid wheat.
The code in this repository is to support reproducibility. It is not designed as stand-allone applications.
The NLR-Annotator, which is also described in this paper can be found here.
Methods to generate supplementary tables S5 and S6
Two files data/ADR1_addon.txt and data/manual_inspection_nlrloci.txt are input data for this code. These files cannot be gererated based on public data alone and are added here.
Methods to generate annotation files for iTOL. Basis for Figures 2, S4, S5 and S6.
Methods to create Figure 3.
Prepare data for ternary plots (Figure 4).
Plot ternary plots for NLR expression
BioSequence.java, BioSequenceReader.java and FastaReader.java are support classes that are used by methods in source code above.