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grayleafspotr - Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images

Quantitative phenotyping of gray leaf spot (Magnaporthe oryzae) fungal colonies grown on petri dishes. The package segments colonies from time-lapse plate photographs using a bundled SmallUNet deep-learning model, extracts morphometric and texture features (area, eccentricity, crack coverage, radial profile), and provides tidy result objects together with template ggplot2 visualisations. Python dependencies are managed automatically through basilisk; no manual environment setup is required.

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softwarepreprocessingvisualizationclassificationfeatureextractionbioconductorbioconductor-packagebiological-data-analysisgrayleafspothuggingfaceimage-processingmlpythonr-universesegmentation

4.78 score 1 stars 6 scripts

grayleafspotr - Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images

Quantitative phenotyping of gray leaf spot (Magnaporthe oryzae) fungal colonies grown on petri dishes. The package segments colonies from time-lapse plate photographs using a bundled SmallUNet deep-learning model, extracts morphometric and texture features (area, eccentricity, crack coverage, radial profile), and provides tidy result objects together with template ggplot2 visualisations. Python dependencies are managed automatically through basilisk; no manual environment setup is required.

Last updated

softwarepreprocessingvisualizationclassificationfeatureextractionbioconductorbioconductor-packagebiological-data-analysisgrayleafspothuggingfaceimage-processingmlpythonr-universesegmentation

4.78 score 1 stars 6 scripts

ExperimentalDesignGeneratorandRandomiser - 'EDGAR': Experimental Design Generator and Randomiser

Native R implementation of 'EDGAR', the Experimental Design Generator and Randomiser. 'EDGAR' was originally developed as a suite of 'Excel' <https://www.microsoft.com/microsoft-365/excel> workbooks by the Biometrics team at Rothamsted Research <http://www.edgarweb.org.uk/>. The algorithms were subsequently re-implemented in the open-source 'Python' <https://www.python.org/> project 'rotsl/edgar' <https://rotsl.github.io/edgar/>, distributed as the 'edgar-design' package on 'PyPI' <https://pypi.org/project/edgar-design/>. This R package is a native R port of that 'Python' implementation: it does not require 'Python', 'reticulate' <https://CRAN.R-project.org/package=reticulate>, or any external service at runtime, and provides deterministic, reproducible randomisation for nine experimental designs including alpha designs (Patterson and Williams, 1976) <doi:10.1093/biomet/63.1.83>. Cross-language reproducibility with the 'Python' implementation is achieved by porting the Mersenne Twister seeding implementation from 'CPython' <https://github.com/python/cpython> and the Fisher-Yates shuffle to native R.

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4.30 score 211 downloads

biotrace - R Integration for the BioTrace GitHub Action

Tools for configuring, validating, running and inspecting integrations with the BioTrace GitHub Action, which traces biological results from data and code to figures and scientific claims. The package provides an R API, a command-line interface, GitHub workflow scaffolding, configuration helpers and report readers. It does not ship or execute the upstream TypeScript engine; BioTrace runs only through its published GitHub Action (uses: rotsl/biotrace@v1).

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bioinformaticsbiotracecomputational-biologycomputational-biology-datasetsgithubgithub-actionshpcr-universescientific-computingworkflows

3.00 score 1 stars 7 scripts

grayleafspotdata - File Manifest for the S-BSST3199 Magnaporthe Colony Image Dataset

Provides a machine-readable file and image manifest for the research data deposited in EMBL-EBI BioStudies under accession S-BSST3199 (a time-series petri-dish image dataset of Magnaporthe colonies from twelve plates, with associated morphometric analysis outputs produced by metrics-petri 3.0.0). The original research files are not bundled in this R package; they remain hosted by BioStudies. The manifest can be used in image-analysis and plant-pathology workflows, including workflows based on the 'grayleafspotr' software. Related research outputs are documented using their persistent identifiers.

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2.70 score 3 scripts 205 downloads