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qrlabelr - Generate Machine- And Human-Readable Plot Labels for Experiments

A no-frills open-source solution for designing plot labels affixed with QR codes. It features 'EasyQrlabelr', a 'BrAPI-compliant' 'shiny' app that simplifies the process of plot label design for non-R users. It builds on the methods described by Wu 'et al.' (2020) <doi:10.1111/2041-210X.13405>.

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experimentsfield-plotslabels-generatorqr-codeshiny-apps

6.26 score 19 stars 24 scripts 324 downloads

linkmapper - Point-and-Click Linkage Mapping and QTL Analysis

A 'shiny' application and a set of plain R functions for building genetic linkage maps and locating quantitative trait loci in F2 intercross, backcross and recombinant inbred line populations. It wraps 'onemap' (Margarido et al. 2007 <doi:10.1111/j.2007.0018-0661.02000.x>) for segregation tests, two-point analysis, grouping, ordering and map estimation, and 'qtl' (Broman et al. 2003 <doi:10.1093/bioinformatics/btg112>) for interval mapping and composite interval mapping with permutation thresholds. Results can be exported as figures, tables, a self-contained HTML report and an R script that reproduces the analysis.

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gene-maplinkage-mappingopen-sourceqtl-mappingr-shiny

2.00 score

clusnalyst - Point-and-Click Cluster Analysis of Molecular and Trait Data

A 'shiny' application and a set of plain R functions for clustering samples from dominant markers, SNP genotypes (CSV, VCF or HapMap), quantitative or mixed traits, and DNA or protein sequences. It computes distance matrices, builds trees by UPGMA, WPGMA, single, complete or Ward linkage, neighbour joining or BIONJ, and checks them with marker bootstrap support (Felsenstein 1985 <doi:10.1111/j.1558-5646.1985.tb00420.x>), cophenetic correlation, average silhouette width, the gap statistic and Mantel tests. It also offers principal coordinates and principal components, k-means and partitioning around medoids, and exports a self-contained HTML report and an R script that reproduces the analysis.

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cluster-analysisphylogeneticsplant-breedingshiny

1.70 score

ggwizard - Create Beautiful ggplot2 Charts Without Coding

A point-and-click Shiny application that guides non-programmers through importing CSV or Excel data, previewing it, and generating publication-quality ggplot2 charts. Supports bar, line, scatter, time series, histogram, box, violin, and area plots with full customisation of labels, themes, colours, and font styles. Outputs are saved to a timestamped folder along with a reproducible R script and a run log.

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data-visualizationggplot2golemno-codeplotlyshiny

1.70 score

FounderForge - Prepare Marker Data as AlphaSimR Founder Populations

A point-and-click Shiny application that helps non-programmers prepare their own marker data (VCF, HapMap, numeric genotype matrices or PLINK) as a founder population for AlphaSimR simulations. It guides users through uploading data, quality-control review, filtering (MAF, missingness, monomorphic markers), optional trait definition and export of the objects required by AlphaSimR::newMapPop(), with progress feedback, helpful errors, optional before/after PCA validation and a full text log of the run.

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alphasimrfounder-populationhapmapplant-breedingshiny-appsimulationvcf

1.70 score