This repository provides the source code for reproducing the results of the study titled " Chromatin dynamics during C. elegans embryogenesis at the single-cell level" by Zhiguang Zhao# , Rong Fan# , Weina Xu, Yangyang Wang, Xuehua Ma, and Zhuo Du*.
- fluorescent_compensation.py Compensation for depth-dependent attenuation of fluorescence intensity during 3D live-cell imaging.
- data_stats.py Calculating the genomic and cellular distribution, coefficient of variation, the information content of GFP expression integrated into different genomic positions.
- CAL_lineage.py Performing analyses related to lineage-dependent changes in chromatin activity landscape.
- CAL_tissue.py Performing analyses related to tissue-based convergence and lineage-dependent heterogeneity in chromatin landscape within the same tissue type.
- CAL_symmetry.py Performing analyses related to chromatin landscape divergences between left-right symmetry cells and their progenitor cells.
- CDCA.py Performing analyses related to chromatin co-dynamic region.
- data folder contains the raw data needed for various analyses.
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)
- numpy (>= 1.19.1)
- scipy (>= 1.2.1)
- statsmodels (>= 0.11.1)
Additional Python packages required for plotting the figures include:
- seaborn (>= 0.11.0)
- matplotlib (>= 3.0.2)
This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.