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Getting Started

Folder Structure

StochasticGene expects a specific directory structure for data and results:

project_root/
├── data/
│   ├── alleles/
│   └── halflives/
└── results/

Setting Up

Use the built-in helper to set up a new project folder with mock data:

using StochasticGene
rna_setup("scRNA")  # Creates the structure in the "scRNA" folder
cd("scRNA")         # Move into the project directory

Fitting a Model

Fit a simple two-state model to the mock data:

fits = fit(G=2, R=0, transitions=([1,2],[2,1]), datatype="rna", datapath="data/HCT116_testdata/")

This will use the default mock data and model settings. For more advanced usage, see the API and Examples sections.

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

Model Types

StochasticGene supports several model types:

  • G models (telegraph models)
  • GR models (with pre-RNA steps)
  • GRS models (with splicing)
  • Coupled models (multiple alleles)

Data Types

The package can handle:

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

Basic Usage Examples

RNA Count Analysis

# Fit a two-state model to RNA count data
fits = fit(
    G = 2,
    R = 0,
    transitions = ([1,2], [2,1]),
    datatype = "rna",
    datapath = "data/",
    gene = "MYC"
)

Live Cell Imaging

# Analyze MS2 reporter data
fits = fit(
    G = 2,
    R = 1,
    transitions = ([1,2], [2,1]),
    datatype = "trace",
    datapath = "data/",
    gene = "MS2"
)

Dwell Time Analysis

# Analyze dwell time distributions
fits = fit(
    G = 2,
    R = 0,
    transitions = ([1,2], [2,1]),
    datatype = "dwell",
    datapath = "data/",
    gene = "PP7"
)

Next Steps