Re-analyzing some data for Tepary bean paper

script used for normalizing the TPA and KAU data from S. pimpinellifolium panel exposed to salt stress in the greenhouse (TPA) or field stress (KAU) conditions.

Little notebook describing the testing of AWWEsmo accuracy across various temperatures

The pipeline for data analysis for CropReporter captured chlorophyll fluorescence.

This notebook describes the analysis of Arabidopsis growth in different soil types

SPIRO experiment for few (three) mutants of Arabidopsis, determined to be homologous to genes identified in Cowpea to be associated with drought resilience

Analysis of the cotton root cross-sections performed in collaboration with Dr. Avat Shekoofa.

This notebook describes some improved data visualization and regression analysis on data collected at The Plant Accelerator (Adelaide, Australia), and pre-processed by Mitch Morton and Helena Oakey.

The Arabidopsis seedlings (Col-0) were transferred to media +/- osmotic stress (PEG8000) that were additionally enriched with the cowpea metabolite extractions from plants exposed to mock / drought stress treatment. This specific experiment describes metabolite extractions performed on UCR779

Notebook describing a detailed time series experiment of lateral root development in wild and cultivated tomato seedlings grown on agar plates +/- 100 mM NaCl

This compiles data analysis pipelines from Hayley Sussman and Aparna Srinivasan into one pipeline, and compares the increase in projected shoot area over time as well as evapotranspiration. These experiments serve mainly as pilot projects to evaluate our Evapotransporation and PhenoCage setups

The notebook describing the data analysis of T-DNA insertion lines in Arabidopsis, screened for drought stress induced changes in evapotranspiration and photosynthetic performance

The notebook describing the analysis and plotting of GWAS data obtained from the analysis of salt stress-induced changes in root:shoot ratio and mapped using 250 k SNPs.

The pipeline describing the data curation and analysis for salt stress-induced changes in root:shoot ratio across Arabidopsis HapMap accessions.

This notebook describes the analysis of the GWAS data generated using the ASReml script for the UCR miniCore cowpea population screened in 2022 by Hayley Sussman. GWAS was performed by Magda Julkowska.

This notebook combines all the data collected for cowpea experiments - starting with side-view images, FW/DW, PhotosynQ data, and evapotranspiration. It is meant to perform final data curation, examination, as well as relationship between the recorded traits.

This notebook describes the data analysis pipeline for side-view images collected for last cowpea screen (Cowpea 06), performend between June 17th and July 21st, 2022 by Hayley Sussman, assisted by high-school research intern, Ting Fei. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This notebook describes the data analysis pipeline for side-view images collected for 5th cowpea screen (Cowpea 05), performed between May 20th and June 23rd, 2022 by Hayley Sussman. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This notebook describes the data analysis pipeline for side-view images collected for 4th cowpea screen (Cowpea 04), performed between April 15th and May 19th, 2022 by Hayley Sussman. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This notebook describes the data analysis pipeline for side-view images collected for 3rd cowpea screen (Cowpea 03), performed between April 1st and May 5th, 2022 by Hayley Sussman. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This notebook describes the data analysis pipeline for side-view images collected for 2nd cowpea screen (Cowpea 02), performed between March 18th and April 21st, 2022 by Hayley Sussman. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This notebook describes the data analysis pipeline for side-view images collected for 1st cowpea screen (Cowpea 01), performend between February 11th and March 15th, 2022 by Hayley Sussman. The data was analyzed using the PlantCV pipeline by Magda Julkowska, and used here as an input.

This pipeline describes analysis of the loci identified through GWAS in wild tomato (S. pimpinellifolium) based on the phenotyping data collected at The Plant Accelerator (TPA) in Adelaide, Australia by Mitchell Morton. The GWAS was performed and analyzed by Magdalena Julkowska for loci overlapping between various measured phenotypic traits, as well as for the pair-wise linkage disequilibrium (LD) within 50kbp from the identified SNPs.

This pipeline describes analysis of the experiment where drought (10% WHC) and salt (100 mM NaCl) were imposed on wild tomato (S. pimpinellifolium), Setaria viridis and cowpea (Vigna unguiculata). The PhotoSynQ measurements and evaotranspiration were taken as measured to indicate physiological differences between plants grown under non-stress conditions (60% WHC) and stress conditions

This analysis pipeline was performed for the experiment where we tested the effect of transferring 6 days old seedlings to 0 / 125 mM NaCl agar plates OR spraying the plates with 0 / 125 mM NaCl solution.

This pipeline describes the first attempt at analyzing the SPIRO grown experiment, analyzed using SPIRO (pre-processing), SmartRoot and BackTracker. The data turned out to be quite noisy, so the pipeline contains multiple solutions to how to deal with the noisiness, noise reduction through smooth splines and finally data visualization.

The analysis of Maryam Rahmati Ishka's experiment for duf247 mutant (at3g50160-5) and Col-0 (wt) grown in soil and imaged on Raspberry Pi PhenoRigs at BTI between October and November 2021.

This R - notebook describes the geographical distribution of the cowpea accessions collected by Dr Alihu Ramatu from University of Ahmadu-Bello in Zaria. The location was plotted by Magda Julkowska to create an overview of all accessions.

This is the analysis of the data that was collected by our collaborators in Nigeria, Alihu Ramatu and colleagues, from University of Ahmadu-Bello in Zaria.

We screened natural diversity panel of 221 accessions of wild tomato (S. pimpinellifolium) for salt stress-induced changes in root architecture. The root architecture was quantified using SmartRoot for 0-4 days after transfer to stress media. Here - we describe the data analysis of the data coming from the SmartRoot files, including the calculations of root architecture traits and growth rate calculations for individual RSA components.

The haplotype analysis of the loci identified by Marina Huber, a PhD student in Prof. Pierink's group, for loci 1, 2, 4 and 6

The haplotype analysis of the loci identified by Marina Huber, a PhD student in Prof. Pierink's group, for loci A, D and K.

Exploring the developmental and heat-stress induced differences in growth of Arabidopsis lines carrying mutations induced by Dr. Bucher's lab. The notebook depicts analysis and data curation steps from plants imaged using Raspberry Pi cameras and quantified using PlantCV pipeline. The work here was performed by Li'ang Yu and Magdalena M. Julkowska. Update to previous version - with among others, fixed growth rate calculations and plotting variance rather than minimum/maximum values for all the lines compared

Exploring the developmental and heat-stress induced differences in growth of Arabidopsis lines carrying mutations induced by Dr. Bucher's lab. The notebook depicts analysis and data curation steps from plants imaged using Raspberry Pi cameras and quantified using PlantCV pipeline. The work here was performed by Li'ang Yu and Magdalena M. Julkowska.

Data analysis pipeline which was used to examine the phenotypes of T-DNA insertion lines located in the GWAS loci associated with Fv'/Fm' and QY max. The data used for this analysis is available at https://doi.org/10.5281/zenodo.3762244

The notebook describes how to get Manhattan and qqplots from the GWAS rad files which were produced for Arabidopsis population

In this notebook I am going to examine the lateral root distribution across a collection of tomato accessions, for which the data were collected by Safarina Ahmad (Testerink lab, UvA/WUR, The Netherlands). The aims are to: 1) examine the lateral root distribution across the main root 2) visualize the shift in apical zone (getting extended under salt stress) that Safarina observed in the pictures 3) calculate the “lateral root center of gravity” - indicating the portion of Main Root at which majority of Lateral Root number / Length standard calculation from center of gravity (physics) is: calculate momentum for each object (dist. * weight) center of gravity = sum(momentum) / sum(distance)

This experiment was performed on Solanum pimpinellifollium accessions showing diverse idiotypes in their root architecture on agar plate assay performed previously. In order to examine the consequences of root idiotype on salinity tolerance, the accessions were grown on hydroponics. More information on the experiment setup in the document.

This is an example of how to process the data that is generated with the PSI high-throughput phenotyping machine - specially prepared for KAUST workshop on data analysis by Magdalena Julkowska - the data used for this purpose is not publicly accessible.

This is an analysis of the tomato root system architecture dynamics. The experiment was performed between 27th of March 2019 and 4th of April 2019, where eight tomato lines were screened for their dynamic response to salt stress, focusing on the root growth dynamics and changes in morphology.

This is an example workflow for analyzing (and curating) the plant phenotypic data coming from the PSI machine. The pipeline is developed using R language and does not require skills beyond the basic R installation guidelines.