/mouse-embeddings

dimensional reduction of mouse phenotype data

Primary LanguageROtherNOASSERTION

mouse-embeddings

This repository holds an analysis of phenotypes associated with mouse models.

The repository describes analyses of large datasets that are not included on github. A bundle that includes the datasets and a copy of the analysis code is available on zenodo (dataset 4916171). The bundle includes raw data files, processed data files, computed results, figures, and source code.

Setup

Directories in the github repository:

  • prep - directory with scripts that process raw data files and perform one-time computations, e.g. database builds and database queries.
  • R - functions used during generation of vignettes
  • vignettes - code for Rmarkdown vignettes, and associated helper files.

Directories not included in the github repository, but included in the data snapshot (and required for running the code from scratch):

  • data - directory with data files pertaining to ontologies, mouse models, and diseases.
  • results - directory with flat data files generated from data.
  • cache - directory with processed data files using in R vignettes.

The vignettes folder contains two Rmarkdown files and several helper files. To compile the vignettes into pdf documents, launch R, install the required packages (see vignettes/config.R) and render the Rmarkdown files.

render("ME_Figures.Rmd")
render("ME_Supplementary.Rmd")