How We Do What We Do
This is an interface to tissue-specific RNA-seq in the staple food crop of cassava. It allows the user to search for genes using multiple keywords and identifiers, and display the expression pattern throughout multiple tissues of the plant. Additional tools allow the user to find whole sets of genes that are up or down regulated in various tissues and even those that are up and down regulated during a xanthamonas infection.
Abiotic Stress Response in Sorghum
http://shiny.danforthcenter.org/Bart_Lab_Sorghum/
https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.23
High-throughput phenotyping produces massive multivariate data and this is a tool created to allow a user to explore one of our published sorghum runs on the Bellwether platform. By point-and-click, the user can selects the phenotype and then trendlines, boxplots, and growth rates are automatically calculated and displayed. In addition to morphology, color profiles are also available and allow for easy identification of nitrogen deficiency.
PhenoAnalyzer
http://shiny.danforthcenter.org/PhenoAnalyzer/
https://github.com/jberry47/Shiny-PhenoAnalyzer
https://www.biorxiv.org/content/10.1101/2021.04.13.437608v1
This tool takes automatic data analysis from our high-throughput Bellwether platform to the next level. Instead of having data built in, the user provides standard output from one of two image analysis suites and computes a huge range of statistics, and visualizations on the given dataset. Analyses are broken out into: summary, diagnostics, shape analysis, VIS analysis, and NIR analysis. Each of these sections have various techniques and visualizations, and provides the user with a complete picture of their data.
Exploring Sorghum-Xanthamonas arms race with dual-rnaseq
http://shiny.danforthcenter.org/bart_dual_rnaseq/
https://github.com/jberry47/Shiny-dual_rnaseq
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009175
Classic output of any RNA-seq experiment are large lists of differentially expressed genes and this tool allows for the computation of intersections of these lists from a dual- sorghum & xanthamonas transcriptomics dataset. The user selects how the intersection is defined and inclusion criteria, and the intersection is created. Additionally, the user can easily visualize the gene or transcript of interest and assess biological significance simply by point-and-click.
In large multi-lab collaboration projects, having a centralized repository is essential for transmission of up-to-date data to everyone in the group. This tool allows for easy access to whole or subsets of data from every lab in the Department of Energy funded Sorghum Systems project. Not only are numerical data available here, but if there is accompanying sequence or image data with a given experiment, that data is also available. In addition to bulk downloads of data, visualizations of the data are available as well to allow even more fluidity between the groups.
In the wake of high-throughput image-based phenotyping, computationally efficient image analysis software is essential for obtaining on-demand data. PhenotyperCV is a header-only C++11 library that contains a large set of functions to easily create workflows for a given task. Along with the headers of functions, the library comes with an executable that already has entire workflows created for image segmentation, machine learning classifiers, standardizing color profiles, and camera calibration.