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Supplemental Code for Forcier et al., 2018
Jupyter Notebook Python
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code
data
figures
manuscript
preprocessing
protocols
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LICENSE.txt
README.md

README.md

Data and analysis scripts for:

Forcier et al. Measuring cis-regulatory energetics in living cells using allelic manifolds. bioRxiv doi:10.1101/380972 (2018)

Directory structure:

  • code/: Python analysis scripts and Jupyter notebooks
  • data/: Metadata, raw data, and processed data for this study
    • constructs/: DNA sequence constructs used in this study
    • literature/: Data extracted from the prior literature
    • plate_reader/: Raw data from plate reader used for Miller assays
    • glycerol_stocks.xlsx: List of glycerol stocks used in this study
  • figures/: Computationally rendered components of the figures in the manuscript.
  • manuscript/: Copy of Precision dissection of cis-regulatory energetics in living cells.
  • preprocessing/: Code and intermediate files for processing raw data
    • data/: Processed data and metadata for this study
      • glycerol_stocks.xlsx: List of glycerol stocks used in this study
      • library_clusters.py: CRP-RNAP spacing library clustering by glycerol stock
      • plate_panel.pkl: Pandas panel of raw Miller assay data, organized by plate
      • seq_spacing.xlsx: Sequence and CRP-RNAP spacing information for glycerol stocks
    • intermediates/: Fits and resamplings of model to processed data
    • results.xlsx: Complete summary of processed data
    • scripts/: Python analysis scripts for preprocessing
      • 18.10.30_init_fits.py: Script for generating the fit of all data for c61, occlusion, and conjoined libraries
      • 18.10.30_param_exp_c61.py: Script for exploring the effects of initial parameter selection on fitted values for c61 library
      • 18.10.30_param_exp_conj.py: Script for exploring the effects of initial parameter selection on fitted values for global fit to all libraries
      • 18.10.30_param_exp_occlusion.py: Script for exploring the effects of initial parameter selection on fitted values for occlusion library
      • 18.10.30_resamp_beta.py: Script for resampling all libraries for \beta' values
      • 18.10.30_resamp_c61.py: Script for resampling the library with CRP at -61.5
      • 18.10.30_resamp_cAMP_dilution.py: Script for resampling the data taken with varying cAMP concentrations for c71 and occlusion libraries
      • 18.10.30_resamp_conj.py: Script for resampling the global fit to all libraries
      • 18.10.30_resamp_occlusion.py: Script for resampling the library of constructs with CRP binding occluding the RNAP binding site
      • 18.10.30_summary_gen.py: Script for consolidating all intermediate processed data into summaries and results.xlsx
      • plate_processor.py: Script for processing raw data and generating plate_panel.pkl
  • protocols/: Primary protocols used in this study
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