Human eyeIntegration >= v2.0 Shiny App

Updated to serve the 2023 data update. New samples. Metadata cleaning. Recount3-based quantification

Web app

https://eyeIntegration.nei.nih.gov

scEiaD based sqlite file:

https://hpc.nih.gov/~mcgaugheyd/eyeIntegration/scEiaD.2023_03_02.sqlite.gz

Files for use in PCA Visualization can be found here:

https://hpc.nih.gov/~parikhpp/eyeIntegration_app_v2/eye_pca_data.RData.gz https://hpc.nih.gov/~parikhpp/eyeIntegration_app_v2/eye_pca_data_with_GTEx.RData.gz https://hpc.nih.gov/~parikhpp/eyeIntegration_app_v2/eye_percentVar_data.RData.gz

Updated PCA Files (03-28-23)

https://hpc.nih.gov/~parikhpp/eyeIntegration_app_v2/EiaD_pca_analysis.Rdata.gz https://hpc.nih.gov/~parikhpp/eyeIntegration_app_v2/eyeIntegration_2023_pca.RData.gz

All below relates to the 2019 and earlier data

We plan on updating the data pulling to put everything in the same place

Install locally and run in three steps:

Warning! get_eyeIntegration_datasets() currently downloads ~20 GB of data and requires ~65 GB of space, uncompressed.

devtools::install_github('davemcg/eyeIntegration_app')
eyeIntegrationApp::get_eyeIntegration_datasets()
eyeIntegrationApp::run_eyeIntegration()

Install locally (custom location!) and run in three steps:

devtools::install_github('davemcg/eyeIntegration_app')
eyeIntegrationApp::get_eyeIntegration_datasets(destdir='/your/path/to/app')
eyeIntegrationApp::run_eyeIntegration(app_path='/your/path/to/app')

Already have the most recent SQLite databases and just need new web app resources?

devtools::install_github('davemcg/eyeIntegration_app')
eyeIntegrationApp::get_eyeIntegration_datasets(file = "eyeIntegration_v101_01_lightweight.tar.gz",
                                                       destdir='/your/path/to/app')
eyeIntegrationApp::run_eyeIntegration(app_path='/your/path/to/app')

Where's the 45 GB of data going, by default?

system.file('app', package = 'eyeIntegrationApp')