Outputs

This pipeline tool creates several directories in the specified output directory. Below is a list and description of these output directories with links to more detailed information.

Overview of Cell Maps Pipeline which shows PPI and image download followed by embedding, coembedding, and finally hierarchy generation

When run via SLURM the following directories and files are created:

List of main folders created by tool on left and on right the scripts needed by SLURM

Within each directory are some common files:

list of common files created in each directory

1.image_download

Output from cellmaps_imagedownloader, for more information on output click here

list of common files created in 1.image_download directory

1.ppi_download

Output from cellmaps_ppidownloader, for more information on output click here

list of common files created in 1.ppi directory

2.ppi_embedding

Output from cellmaps_ppi_embedding, for more information on output click here

list of common files created in 2.ppi_embedding directory

2.image_embedding_fold#

Output from cellmaps_image_embedding, for more information on output click here

list of common files created in 2.image_embedding_fold# directories

3.coembedding_fold#

Output from cellmaps_coembedding, for more information on output click here

list of common files created in 3.coembedding_fold# directories

4.hierarchy

Output from cellmaps_generate_hierarchy, information on output click here

list of common files created in 4.hierarchy directories

5.hierarchyeval

Output from cellmaps_generate_hierarchy, information on output click here

list of common files created in 5.hierarchyeval directories