Browse Tools
U2OS Cell Map
Tools for cell map construction
- Cell map map pipeline
- This package is used to invoke steps of the cell map construction pipeline, including downloading data, generating embeddings, unsupervised co-embedding, and creating the final cell map hierarchy.
- Image downloader
- This package downloads images from the Human Protein Atlas or other user-supplied links
- PPI downloader
- This package loads in a protein-protein interaction network and prepares the data for embedding
- Generate image embedding
- This package creates an image embedding using the densenet model (see Tools for image embedding section below)
- Generate PPI embedding
- This package creates an embedding for each protein in a protein-protein interaction netowrk using node2vec
- 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
- Generate hierarchy
- This package constructs a hierarchy using pan-resolution community detection with HiDeF
- Cell maps utils
- This package contains utilities needed by the various tools