API Reference

Core Functions

Model Fitting

• fit: Main function for fitting models to data
• fit_parallel: Parallel version of fit for large datasets

Data Analysis

• analyze_results: Analyze fitting results
• plot_results: Plot fitting results
• save_results: Save results to disk

Data Types

RNAData

struct RNAData
    histRNA::Vector{Float64}  # Histogram of RNA counts
    gene::String             # Gene name
    condition::String        # Experimental condition
    nalleles::Int           # Number of alleles
end

A concrete struct for storing RNA histogram data. This is used for steady-state RNA count distributions from techniques like smFISH or scRNA-seq.

Example:

data = RNAData(
    histRNA=[1,2,3,4,5],
    gene="GENE1",
    condition="control",
    nalleles=2
)

• TraceData: Live cell imaging data structure
• DwellTimeData: Dwell time data structure

Model Types

• GMmodel: Gene model structure
• Transformation: Data transformation structure

Utility Functions

• rna_setup: Set up project directory structure
• write_traces: Generate model-predicted intensity traces
• write_ONOFFhistograms: Generate ON/OFF dwell time histograms
• write_residency_G_folder: Generate G state residency probabilities

Model Components

Gene States (G)

• Arbitrary number of gene states
• User-specified transitions between states
• One active state for transcription initiation

Pre-RNA Steps (R)

• Irreversible forward transitions
• mRNA ejection from final R step
• Optional reporter insertion step

Splicing (S)

• Up to R splice sites
• PreRNA with or without spliced intron
• Multiple configurations per R step

Data Types

The package can handle:

• mRNA count distributions (smFISH, scRNA)
• Image intensity traces (live cell imaging)
• Dwell time distributions
• Combined data types