Source Code - RNA gradients can guide condensates toward promoters: Implications for enhancer–promoter contacts and condensate-promoter kissing

Directories Content Directory GitHub Finite Volume Simulations FVM https://github.com/gohdavid/CoupledEPCondensates Theoretical Calculations Theory https://github.com/gohdavid/CoupledEPCondensatesTheory Brownian Dynamics Simulations BD https://github.com/gohdavid/active-polymers Finite Element Method FEM https://github.com/gohdavid/CoupledEPCondensatesFEM Jupyter Notebooks Figure Notebook Fig. 1B FVM/workspace/01_Analysis/Fig_1B.ipynb and FVM/workspace/01_Analysis/Fig_1B_I-II-III.ipynb Fig. 1C Theory/Fig_1C_CSV.ipynb Fig. 2B Theory/Fig_2B-S6-S7-S9-S10.ipynb Fig. 2C BD/Fig_2C-S13.ipynb Fig. 2D BD/Fig_2D-S12.ipynb Fig. 2E FVM/workspace/04_Analysis/Fig_2E.ipynb Fig. 3B FVM/workspace/05_Analysis/Fig_3B-3C.ipynb Fig. 3C FVM/workspace/05_Analysis/Fig_3B-3C.ipynb Fig. 3D FVM/workspace/05_Analysis/Fig_3D.ipynb Fig. 4B Theory/Fig_4B.ipynb Fig. 4C FVM/workspace/05_Analysis/Fig_4C-4D.ipynb Fig. 4D FVM/workspace/05_Analysis/Fig_4C-4D.ipynb Fig. S1 FVM/workspace/01_Analysis/Fig_S1-S2-S3.ipynb Fig. S2 FVM/workspace/01_Analysis/Fig_S1-S2-S3.ipynb Fig. S3 FVM/workspace/01_Analysis/Fig_S1-S2-S3.ipynb Fig. S4 Theory/Fig_S4.ipynb Fig. S5 FVM/workspace/00_Misc/Fig_S5-S15-S16-S17.ipynb Fig. S6 Theory/Fig_2B-S6-S7-S9-S10.ipynb Fig. S7 Theory/Fig_2B-S6-S7-S9-S10.ipynb Fig. S9 Theory/Fig_2B-S6-S7-S9-S10.ipynb Fig. S10 Theory/Fig_2B-S6-S7-S9-S10.ipynb Fig. S11 FEM/Fig_S11.ipynb Fig. S12 BD/Fig_2D-S12.ipynb Fig. S13 BD/Fig_2C-S13.ipynb Fig. S14 FVM/Fig_S14.ipynb Fig. S15 FVM/workspace/00_Misc/Fig_S5-S15-S16-S17.ipynb Fig. S16 FVM/workspace/00_Misc/Fig_S5-S15-S16-S17.ipynb Fig. S17 FVM/workspace/00_Misc/Fig_S5-S15-S16-S17.ipynb Fig. S18 FVM/workspace/05_Analysis/Fig_S18-S19-S20.ipynb Fig. S19 FVM/workspace/05_Analysis/Fig_S18-S19-S20.ipynb Fig. S20 FVM/workspace/05_Analysis/Fig_S18-S19-S20.ipynb Fig. S21 FVM/workspace/05_Analysis/Fig_S21.ipynb