References

Plant Data Visualization Tool Bundles

• ELIXIR Plant Data Orthology/Visualization Bundle - Overview

• ELIXIR TeSS - Materials

• Increasing Plant Bundle - Workshops

Bundle Tools (cork oak data compatible)

• Mercator4 - Bolger, M., Schwacke, R., & Usadel, B. (2021). MapMan Visualization of RNA-Seq Data Using Mercator4 Functional Annotations. In D. Dobnik, K. Gruden, Ž. Ramšak, & A. Coll (Eds.), Solanum tuberosum: Methods and Protocols (pp. 195–212). Springer US. https://doi.org/10.1007/978-1-0716-1609-3_9

• MapMan App - Schwacke, R., Ponce-Soto, G. Y., Krause, K., Bolger, A. M., Arsova, B., Hallab, A., Gruden, K., Stitt, M., Bolger, M. E., & Usadel, B. (2019). MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. Molecular Plant, 12(6), 879–892. https://doi.org/10.1016/j.molp.2019.01.003

• DiNAR - Zagorščak, M., Blejec, A., Ramšak, Ž., Petek, M., Stare, T., & Gruden, K. (2018). DiNAR: Revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R. Plant Methods, 14(1), 78. https://doi.org/10.1186/s13007-018-0345-0

• Ensembl Plants - Ensembl Plants Website

Additional Tools

• Seidr - Schiffthaler, B., Zalen, E. van, Serrano, A., Street, N., & Delhomme, N. (2021). Seiðr: Efficient Calculation of Robust Ensemble Gene Networks. <https://doi.org/10.1101/250696

• Cytoscape - Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303

Biological Data

• Cork Oak Co-expression Network - Barros, P. M., Sapeta, H., Lucas, D., Rodrigues, H., & Oliveira, M. (2022, July 7). Identification of cork oak genetic modules regulating phellem development in response to drought. https://doi.org/10.5281/zenodo.7225240

• Cork Oak Seasonal Growth - Fernández-Piñán, S., Boher, P., Soler, M., Figueras, M., & Serra, O. (2021). Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation. Scientific Reports, 11(1), 12053. https://doi.org/10.1038/s41598-021-90938-5