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PLatform for Analysis of scEiad

What is this?

The code-base for plae.nei.nih.gov

By cloning this repo and downloading (see below) the scEiaD database, you can run PLAE on your local computer.

Warning

scEiaD is a sqlite file that is approximately 420GB when uncompressed. Not a typo!

Installation (bash)

  • You'll need magick otherwise the package install will fail

Installation (in R)

  • Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true") #otherwise some warnings will, by default, be converted to errors (r-lib/remotes#403)
  • remotes::install_github('davemcg/plaeApp')
  • Get scEiaD (run in bash/Terminal) and the metadata in FST
wget http://hpc.nih.gov/~mcgaugheyd/scEiaD/2021_11_11/MOARTABLES__anthology_limmaFALSE___6000-counts-universe-batch-scVIprojection-10-15-0.1-50-20.sqlite.gz
wget http://hpc.nih.gov/~mcgaugheyd/scEiaD/2021_11_11/meta_filter.fst
  • Decompress sqlite file
pigz -d -p 8 MOARTABLES__anthology_limmaFALSE___6000-counts-universe-batch-scVIprojection-10-15-0.1-50-20.sqlite.gz
  • Edit absolute path to sqlite file in inst/app/server.R

Note

  • If you've cloned this repo, then you can create the meta_filter.fst file yourself by running Rscript ~/path/to/plaeApp/src/convert_metadata_to_fst.R /path/to/scEiaD.sqlite /output/path/meta_filter.fst