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ATAC_post-processing.ipynb
ATAC_post-processing.ipynb
 
 
Ext_Fig4_agg.ipynb
Ext_Fig4_agg.ipynb
 
 
Fig1_FACSplots-example.ipynb
Fig1_FACSplots-example.ipynb
 
 
Fig4_ATAC_peaks.ipynb
Fig4_ATAC_peaks.ipynb
 
 
Fig4_atac_tobias.ipynb
Fig4_atac_tobias.ipynb
 
 
Fig5_loopspiles_strength.ipynb
Fig5_loopspiles_strength.ipynb
 
 
Fig5_scaling.ipynb
Fig5_scaling.ipynb
 
 
Figure-ID-and-loops.ipynb
Figure-ID-and-loops.ipynb
 
 
Figure2A-Heatmap_panels-Reverse.ipynb
Figure2A-Heatmap_panels-Reverse.ipynb
 
 
Figure2B-native-anchor-stackups.ipynb
Figure2B-native-anchor-stackups.ipynb
 
 
Figure2C-Heatmap_n_tracks.ipynb
Figure2C-Heatmap_n_tracks.ipynb
 
 
Figure2E_pileups_plotting.ipynb
Figure2E_pileups_plotting.ipynb
 
 
Figure2F-saddles-discrete_cCRE.ipynb
Figure2F-saddles-discrete_cCRE.ipynb
 
 
Figure3C-Heatmap-timecourse.ipynb
Figure3C-Heatmap-timecourse.ipynb
 
 
Figure3D-native-anchor-stackups-CYTO.ipynb
Figure3D-native-anchor-stackups-CYTO.ipynb
 
 
Figure3D_pileups_timecourse.ipynb
Figure3D_pileups_timecourse.ipynb
 
 
Figure5H-prunning-pileups.ipynb
Figure5H-prunning-pileups.ipynb
 
 
Figure6B-saddles-EV1.ipynb
Figure6B-saddles-EV1.ipynb
 
 
Figure6D-saddles-IPG.ipynb
Figure6D-saddles-IPG.ipynb
 
 
FigureSupp1-SampleStats.ipynb
FigureSupp1-SampleStats.ipynb
 
 
FigureSupp2-MCD-detection.ipynb
FigureSupp2-MCD-detection.ipynb
 
 
Generate-Insulation-tracks.ipynb
Generate-Insulation-tracks.ipynb
 
 
Generate-MCD-interactions.ipynb
Generate-MCD-interactions.ipynb
 
 
Generate-extrusion-dots-and-domains.ipynb
Generate-extrusion-dots-and-domains.ipynb
 
 
Generate_ID_allXall_pileups.ipynb
Generate_ID_allXall_pileups.ipynb
 
 
Generate_all_eigenvector_tracks-Copy1.ipynb
Generate_all_eigenvector_tracks-Copy1.ipynb
 
 
Generate_all_eigenvector_tracks.ipynb
Generate_all_eigenvector_tracks.ipynb
 
 
Generate_saddles-EV.ipynb
Generate_saddles-EV.ipynb
 
 
Generate_saddles-discrete_IPGasis.ipynb
Generate_saddles-discrete_IPGasis.ipynb
 
 
Generate_saddles-discrete_IPGwIDs-.ipynb
Generate_saddles-discrete_IPGwIDs-.ipynb
 
 
Generate_saddles-discrete_cCRE.ipynb
Generate_saddles-discrete_cCRE.ipynb
 
 
README.md
README.md
 
 
data_catalog.py
data_catalog.py
 
 
helper_func.py
helper_func.py
 
 
saddle.py
saddle.py
 
 

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inherited-folding-programs

Supplementary code repository for the manuscript: "Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm" by A. Schooley et. al

Most code is deposited in the form of jupyter notebooks and named after associated Figure in the manuscript.

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