This version is modified based on the CSHMM tool and the web visualization tool developed and implemented by Chieh Lin & Jun Ding and is associated with the published work [1] (refered to as Lin & Ding version).

See the original CSHMM for setting up the environments.

1. generate initialization file by using run_init.q
2. run CSHMM using run_cshmm.q.
3. for visualization

• generate .json files for visualization by running run_json.q.
• copy .json files to the web_visualization folder and rename them as data.json and CellViz.json.
• generate .db (database) by runing run_create_table.sh and move it to ht_bin folder.
• boot server using simpleServer.py.

1. Enable initialize the model using existing cell type labels
2. In the web visualization,

• enable displaying the average expression level of a TF's targets per path
• for each DE gene, enable displaying the TFs regulating it in the DE results
• change the coloring rules to color all cells with darker color indicating higher expression.
• enable displaying average expression per path
• enable downloading TFs and eTFs.

Initial contributors:

• Chieh Lin
• Jun Ding

Other contributors:

• Dora Li

1. Update the readme.pdf file for the web visualization tool.

[1] Hurley, Killian, Jun Ding, Carlos Villacorta-Martin, Michael J. Herriges, Anjali Jacob, Marall Vedaie, Konstantinos D. Alysandratos, et al. 2020. “Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.” Cell Stem Cell 26 (4): 593–608.e8.