/multiOmics-integration

Potato ‘omics data analysis pipelines

Primary LanguageHTMLMIT LicenseMIT

‘multiOmics data analysis, integration, and visualisation protocol

  • Data integration and modelling with R
  • Systems biology analysis and visualization pipeline in R and Python

Data management framework

pISA-tree on GitHub

Petek, M., Zagorščak, M., Blejec, A. et al. pISA-tree - a data management framework for life science research projects using a standardised directory tree. Sci Data 9, 685 (2022). https://doi.org/10.1038/s41597-022-01805-5

Expected measurements

Factorial experiment:

  • one or multiple genotypes AND/OR

  • under single and multiple abiotic/biotic stressors AND/OR

  • experiment duration: hours, days, ... : time-series experimental design AND/OR

  • tissue: single or multiple

  • Omics' strategies:

    • Hormonomics
    • Transcriptomics
    • Proteomics
    • Metabolomics
    • Phenomics
    • ...

  • Combination of targeted and untargeted measurements

  • Phenomics data should be preprocessed, i.e. this protocol does not include image analysis

Analysis

Protocol for the integration of multi-omics data and deep phenotyping of potato cv. Désirée under single- and combined abiotic stress responses is available at _p_ADAPTOmics