MuSIC Project

Browse MuSIC Tools

MuSIC Tools

    This page contains links to the various tools used to construct MuSIC maps. This page will be updated as new MuSIC maps and associated pipelines are released.

Tools for MuSIC map construction

  • MuSIC map pipeline
      This package is used to invoke steps of the MuSIC map construction pipeline, including downloading data, generating embeddings, unsupervised co-embedding, and creating the final MuSIC map hierarchy.
      GitHub    Documentation
  • Image downloader
      This package downloads images from the Human Protein Atlas or other user-supplied links
      GitHub    Documentation
  • PPI downloader
      This package loads in a protein-protein interaction network and prepares the data for embedding
      GitHub    Documentation
  • Generate image embedding
      This package creates an image embedding using the densenet model (see Tools for image embedding section below)
      GitHub    Documentation
  • Generate PPI embedding
      This package creates an embedding for each protein in a protein-protein interaction netowrk using node2vec
      GitHub    Documentation
  • Co-embedding
      This package uses unsupervised machine learning to integrate the image and PPI embeddings into a single co-embedding for each protein based on an implementation of MUSE
      GitHub    Documentation

Tools for image embedding

  • Single cell embedding
      This GitHub repository contains code for running the winning model from the Human Protein Atlas Single-Cell Classification Kaggle challenge (Le et al., Nature Methods 2022)

Tools for HEK293 MuSIC Map v1.0

  • MuSIC v1.0 map construction
      This GitHub repository contains code and a step-by-step guide for constructing MuSIC maps using the v1.0 pipeline (Qin et al., Nature 2021), which includes supervised machine learning trained with the Gene Ontology.