grayleafspotr
This is the development version of grayleafspotr; to use it, please install the devel version of Bioconductor.
Quantitative Analysis of Gray Leaf Spot Colonies from Plate Images
Bioconductor version: Development (3.24)
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.
Author: Rohan R [aut, cre, cph]
Maintainer: Rohan R <phonics-tiffs1i at icloud.com>
citation("grayleafspotr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("grayleafspotr")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("grayleafspotr")| Getting Started with grayleafspotr | HTML | R Script |
| grayleafspotr Workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, FeatureExtraction, Preprocessing, Software, Visualization |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Apache License (>= 2.0) | file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | basilisk, reticulate, dplyr, ggplot2, jsonlite, readr, tibble, png, BiocFileCache, EBImage, stats |
| System Requirements | |
| URL | https://rotsl.github.io/grayleafspotr https://github.com/rotsl/grayleafspotr |
| Bug Reports | https://github.com/rotsl/grayleafspotr/issues |
See More
| Suggests | knitr, rmarkdown, pkgdown, magick, jpeg, tiff, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | grayleafspotr_0.99.12.tar.gz |
| Windows Binary (x86_64) | grayleafspotr_0.99.12.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | grayleafspotr_0.99.12.tgz |
| macOS Binary (sonoma-arm64) | grayleafspotr_0.99.12.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/grayleafspotr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/grayleafspotr |
| Bioc Package Browser | https://code.bioconductor.org/browse/grayleafspotr/ |
| Package Short Url | https://bioconductor.org/packages/grayleafspotr/ |
| Package Downloads Report | Download Stats |