Here we provide snippets of the custom code for the manuscript:
"Analysis of Wild Tomato Introgression Lines Elucidates the Genetic Basis of Transcriptome and Metabolome Variation Underlying Fruit Traits and Pathogen Response"
Jędrzej Szymański(1,2*+), Samuel Bocobza(1,3*), Sayantan Panda(1,4*), Prashant Sonawane(1), Pablo D. Cárdenas(5), Justin Lashbrooke(6), Avinash Kamble(7), Nir Shahaf(1), Sagit Meir(1), Arnaud Bovy(8), Jules Beekwilder(9), Yury Tikunov(8), Irene Romero de la Fuente(8,10), Dani Zamir(11), Ilana Rogachev(1) and Asaph Aharoni(1+)
1. Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
2. Current address: Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
3. Current address: Institute of Plant Sciences, Agricultural Research Organization, Institute of Plant Sciences, Rishon LeTzion, Israel
4. Gilat Research Center, Agricultural Research Organization, Mobile Post Negev, 85280 Israel
5. Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
6. Institute for Wine Biotechnology, Faculty of Agrisciences, Stellenbosch University, South Africa
7. Savirtibai Phule Pune University, Department of Botany, Pune, India
8. Wageningen Plant Research, Department of Plant Breeding, Wageningen, Netherlands
9. Wageningen Plant Research, BU Bioscience, Wageningen, Netherlands
10. Current address: Institute of Food Science, Technology and Nutrition, Madrid, Spain
11. Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
published in: Nature Genetics vol XXX
The full methods description is provided in the Methods section of the manuscript and the Supplemental Materials. Scripts provided here use exemplary processed data (folder /data).
The full transcriptome data is available publicly from a GEO repository under accession number: GSE151451
The full metabolome data is available from e!DAL repository under accession number: XXXXX
All results of the study can be browsed interactively in a dedicated online "kILBIL" browser: https://szymanskilab.shinyapps.io/kilbil/