This repository contains the source code for a brief description of the analyses of our study titled "A 4D Single-Cell Protein Atlas of Transcription Factors Delineates Spatiotemporal Patterning During Embryogenesis" by Xuehua Ma#, Zhiguang Zhao#, Long Xiao#, Weina Xu, Yahui Kou, Yanping Zhang, Gang Wu, Yangyang Wang, and Zhuo Du*
- Lineage_specificity.py Brief description for identifying lineage specific TF.
- AP_asymmetry.py Brief description for identifying AP asymmetry TF.
- Tissue_specificity.py Brief description for identifying tissue specific TF.
- Transient_expression.py Brief description for identifying transient expression TF.
- Expression_similarity.py Performing analyses for calculating similarity between two TFs.
- Umap_and_louvain.py Performing analyses related to ontologically-related cells.
- Cell_lineage_distance.py Calculating cell lineage distance between cells.
- Cell_state_divergence.py Calculating cell state divergences .
- data folder contains the raw data needed for various analysis.
All the dependencies are listed in requirements.txt.
Most analyses were performed under python 3.7.1
Additional Python packages required for analysis include:
- pandas (>= 1.0.3)
- scipy (>= 1.2.1)
- umap (>= 0.4.6)
- sklearn (>= 0.23.1)
- community (>= 0.13)
- networkx (>= 2.2)
This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.