From 77d0c2ad5a7e64d1c895c5534caa17cb72ea8eb8 Mon Sep 17 00:00:00 2001 From: Alexander Sandercock <39815775+alex-sandercock@users.noreply.github.com> Date: Sat, 28 Dec 2024 10:35:04 -0500 Subject: [PATCH] Update README.md --- README.md | 162 ++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 110 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index 1f3f10d..e275799 100644 --- a/README.md +++ b/README.md @@ -1,74 +1,132 @@ [![R-CMD-check](https://github.com/Breeding-Insight/BIGapp/workflows/R-CMD-check/badge.svg)](https://github.com/Breeding-Insight/BIGapp/actions) -[![Development](https://img.shields.io/badge/development-active-blue.svg)](https://img.shields.io/badge/development-active-blue.svg) - +[![Development Status](https://img.shields.io/badge/development-active-blue.svg)](https://img.shields.io/badge/development-active-blue.svg) + -# (B)reeding (I)nsight (G)enomics app +
-The BIGapp is a user-friendly tool for processing low to mid-density genotyping data for diploid and polyploid species. This R shiny app provides a web-based user friendly way for users to analyze genomic data without needing to use command-line tools. Additional analysis will be added, with the initial focus on a core set of features for supporting breeding decisions. +# (B)reeding (I)nsight (G)enomics app (BIGapp) -### Supported Analyses + -Initial supported analyses will include the mature genomics/bioinformatics pipelines developed within Breeding Insight, with additional analyses continuing to be added. +
-Supported: -- Genotype processing - - Dosage call from read counts - - SNP filtering - - Sample filtering -- Summary metrics - - SNP Polymorphism Information Content - - SNP Minor Allele Frequency - - Sample Observed Heterozygosity -- Population Structure - - PCA - - DAPC -- GWAS - - GWASpoly -- GS - - Estimate Model Prediction Accuracy - - Predict Phenotype Values and EBVs for Samples +BIGapp is a user-friendly web application built with R and Shiny, designed to simplify the processing of low to mid-density genotyping data for both diploid and polyploid species. It provides a powerful and intuitive interface for researchers and breeders to analyze genomic data without requiring command-line expertise. -### Running the BIG app +## Key Features -Tutorial available: -https://scribehow.com/page/BIGapp_Tutorials__FdLsY9ZxQsi6kgT9p-U2Zg +- **Web-Based Interface:** Access BIGapp through your web browser, eliminating the need for complex software installations. +- **Genotype Processing:** + - Call genotypes from read counts. + - Filter SNPs based on various criteria. + - Filter samples to ensure data quality. +- **Summary Statistics:** + - Calculate SNP Polymorphism Information Content (PIC). + - Determine SNP Minor Allele Frequency (MAF). + - Compute Sample Observed Heterozygosity. +- **Population Structure Analysis:** + - Perform Principal Component Analysis (PCA). + - Conduct Discriminant Analysis of Principal Components (DAPC). +- **Genome-Wide Association Studies (GWAS):** + - Utilize GWASpoly for robust association mapping. +- **Genomic Selection (GS):** + - Estimate model prediction accuracy. + - Predict phenotypic values and Estimated Breeding Values (EBVs) for your samples. +- **Expanding Functionality:** BIGapp is actively developed, with new analyses and features continuously being added. -Online preview: -https://big-demo.shinyapps.io/bigapp/ +## User Interface -**Local computer** -1. Install R -2. Open Terminal (on mac) -3. To install and run development version of package: -(in terminal) -``` -install.packages("devtools") #If not already installed -devtools::install_github("Breeding-Insight/BIGapp") -BIGapp::run_app() -``` -4. View shiny app in browser +

+ BIGapp Screenshot +
+ BIGapp's intuitive interface makes genomic data analysis accessible to everyone. +

-**Online (in progress)** +## Getting Started -## Third-party software +### Tutorials +New to BIGapp? Check out our comprehensive tutorial to guide you through the process: [BIGapp Tutorials](https://scribehow.com/page/BIGapp_Tutorials__FdLsY9ZxQsi6kgT9p-U2Zg) -The BIG app relies on both custom scripts and previously developed R packages cited below: +### Online Preview -* [R](): version 4.2.2 +Try out a live demo of BIGapp here: [BIGapp Demo](https://big-demo.shinyapps.io/bigapp/) -#### R packages +### Local Installation -* Shiny tools: [shiny](https://cran.r-project.org/web/packages/shiny/index.html), [shinyWidgets](https://cran.r-project.org/web/packages/shinyWidgets/index.html), [shinyalert](https://cran.r-project.org/web/packages/shinyalert/index.html), [shinyjs](https://cran.r-project.org/web/packages/shinyjs/index.html), [shinydisconnect](https://cran.r-project.org/web/packages/shinydisconnect/index.html), [shinycssloaders](https://cran.r-project.org/web/packages/shinycssloaders/index.html), [bs4Dash](https://cran.r-project.org/web/packages/bs4Dash/index.html), [DT](https://cran.r-project.org/web/packages/DT/index.html), [config](https://cran.r-project.org/web/packages/config/index.html) +1. **Install R:** Download and install the latest version of R from [CRAN](https://cran.r-project.org/). +2. **Open Terminal (macOS/Linux) or R Console (Windows).** +3. **Install and Run:** + ```R + if (!requireNamespace("devtools", quietly = TRUE)) + install.packages("devtools") + devtools::install_github("Breeding-Insight/BIGapp") + BIGapp::run_app() + ``` +4. **Access in Browser:** The BIGapp interface will open in your default web browser. -* Genetic analysis: [updog](https://cran.r-project.org/web/packages/updog/index.html), [GWASpoly](https://github.com/jendelman/GWASpoly), [AGHmatrix](https://cran.r-project.org/web/packages/AGHmatrix/index.html), [rrBLUP](https://cran.r-project.org/web/packages/rrBLUP/index.html), [BIGr](https://github.com/Breeding-Insight/BIGr), [adegenet](https://cran.r-project.org/web/packages/adegenet/index.html), [vcfR](https://cran.r-project.org/web/packages/vcfR/index.html) +### Online Deployment (Coming Soon) -* Data manipulation optimization: [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html), [tidyr](https://cran.r-project.org/web/packages/tidyr/index.html), [purrr](https://cran.r-project.org/web/packages/purrr/index.html), [stringr](https://cran.r-project.org/web/packages/stringr/index.html), [future](https://cran.r-project.org/web/packages/future/index.html), [tibble](https://cran.r-project.org/web/packages/tibble/vignettes/tibble.html) +BIGapp will be deployed on USDA SciNet for convenient online access. Stay tuned for updates! -* Statistical analysis: [factoextra](https://cran.r-project.org/web/packages/factoextra/index.html), [MASS](https://cran.r-project.org/web/packages/MASS/index.html), [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html), [matrixcalc](https://cran.r-project.org/web/packages/matrixcalc/index.html) +## Dependencies -* Generate pretty graphics: [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html), [scales](https://cran.r-project.org/web/packages/scales/index.html), [RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/index.html), [plotly](https://cran.r-project.org/web/packages/plotly/index.html) - +BIGapp leverages a powerful suite of R packages: -## Funding Sources -Breeding Insight is funded by USDA through Cornell University. +### Core R Packages + +- **R (>= 4.2.2)** + +### Shiny Framework + +- [shiny](https://cran.r-project.org/web/packages/shiny/index.html): Web application framework. +- [shinyWidgets](https://cran.r-project.org/web/packages/shinyWidgets/index.html): Custom input widgets. +- [shinyalert](https://cran.r-project.org/web/packages/shinyalert/index.html): Create elegant pop-up messages. +- [shinyjs](https://cran.r-project.org/web/packages/shinyjs/index.html): Enhance Shiny apps with JavaScript actions. +- [shinydisconnect](https://cran.r-project.org/web/packages/shinydisconnect/index.html): Handle user disconnections gracefully. +- [shinycssloaders](https://cran.r-project.org/web/packages/shinycssloaders/index.html): Add CSS loaders for visual feedback. +- [bs4Dash](https://cran.r-project.org/web/packages/bs4Dash/index.html): Bootstrap 4 dashboard components. +- [DT](https://cran.r-project.org/web/packages/DT/index.html): Display data tables with interactive features. +- [config](https://cran.r-project.org/web/packages/config/index.html): Manage environment-specific configurations. + +### Genetic Analysis + +- [updog](https://cran.r-project.org/web/packages/updog/index.html): Genotype polyploid individuals. +- [GWASpoly](https://github.com/jendelman/GWASpoly): Conduct GWAS in polyploids. +- [AGHmatrix](https://cran.r-project.org/web/packages/AGHmatrix/index.html): Compute genomic relationship matrices. +- [rrBLUP](https://cran.r-project.org/web/packages/rrBLUP/index.html): Perform genomic prediction. +- [BIGr](https://github.com/Breeding-Insight/BIGr): Breeding Insight's core genomic analysis functions. +- [adegenet](https://cran.r-project.org/web/packages/adegenet/index.html): Explore and analyze genetic data. +- [vcfR](https://cran.r-project.org/web/packages/vcfR/index.html): Manipulate and analyze VCF files. + +### Data Manipulation + +- [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html): Data manipulation tools. +- [tidyr](https://cran.r-project.org/web/packages/tidyr/index.html): Tidy your data. +- [purrr](https://cran.r-project.org/web/packages/purrr/index.html): Functional programming toolkit. +- [stringr](https://cran.r-project.org/web/packages/stringr/index.html): String manipulation. +- [future](https://cran.r-project.org/web/packages/future/index.html): Unified parallel and distributed processing. +- [tibble](https://cran.r-project.org/web/packages/tibble/vignettes/tibble.html): Modern data frame alternative. + +### Statistical Analysis + +- [factoextra](https://cran.r-project.org/web/packages/factoextra/index.html): Extract and visualize multivariate analyses. +- [MASS](https://cran.r-project.org/web/packages/MASS/index.html): Statistical functions and datasets. +- [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html): Sparse and dense matrix operations. +- [matrixcalc](https://cran.r-project.org/web/packages/matrixcalc/index.html): Matrix calculus functions. + +### Visualization + +- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html): Create elegant data visualizations. +- [scales](https://cran.r-project.org/web/packages/scales/index.html): Graphical scaling methods. +- [RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/index.html): Color palettes for thematic maps. +- [plotly](https://cran.r-project.org/web/packages/plotly/index.html): Create interactive web graphics. + +## Funding + +BIGapp development is supported by [Breeding Insight](https://www.breedinginsight.org/), a USDA-funded initiative based at Cornell University. + +## Citation + +If you use BIGapp in your research, please cite: + +Sandercock, Alexander M., Cristiane Taniguti, Josue Chinchilla-Vargas, Shufen Chen, Manoj Sapkota, Meng Lin, Dongyan Zhao, and Breeding Insight Team. 2024. “BIGapp: Breeding Insight Genomics Shiny Application.”