sortscore

Documentation Index

Installation

Option 1: Using a virtual environment (recommended)

# Create and activate a virtual environment
python -m venv sortscore-env
source sortscore-env/bin/activate  # On Windows: sortscore-env\Scripts\activate

# Install sortscore
pip install git+https://github.com/dbaldridge-lab/sortscore.git

Option 2: Using conda/anaconda

# Activate your conda environment
conda activate your-env-name

# Verify you're using conda's pip
which pip  # Should show path to conda environment

# Install sortscore
pip install git+https://github.com/dbaldridge-lab/sortscore.git

Option 3: Install directly (may require adding scripts directory to PATH)

pip install git+https://github.com/dbaldridge-lab/sortscore.git

Usage

With virtual environment or conda environment activated:

sortscore --config path/to/config.json

Otherwise:

python -m sortscore --config path/to/config.json

Testing and Development

See CONTRIBUTING.md for instructions on:

• Installing from a cloned repository
• Running tests with example fixtures
• Using the package in Jupyter notebooks
• Python API examples

Troubleshooting

Having installation or usage issues? See TROUBLESHOOTING.md for solutions to common problems.

Config Templates

config.json

• define additional parameters impacting the analysis execution and outputs

experiment_setup.csv

• define replicates and bins for each sample
• provide parameters for each sample (MFI, cell counts, etc.)

System Requirements

• Python 3.10+
• See requirements.txt for dependencies

flowchart TB
    %% Entry Points
    CLI(("CLI: run_analysis.py")):::entry
    API(("API: sortscore")):::entry

    %% Data Stores
    Config(("Config Files<br/>(JSON/CSV)")):::data
    RawData(("Counts Files<br/>(CSV/Parquet)")):::data
    
    %% Pipeline Stages
    subgraph "Pipeline Stages"
        direction TB
        EL["Experiment Loader"]:::pipelineStage
        DP["Data Processing"]:::pipelineStage
        FL["Filtering"]:::pipelineStage
        NM["Normalization"]:::pipelineStage
        AN["Annotation"]:::pipelineStage
        SC["Scoring"]:::pipelineStage
        EX["Export"]:::pipelineStage
        Utils["Utils"]:::pipelineStage
    end

    %% Visualization
    subgraph "Visualization" 
        direction TB
        VH["Heatmap generate_heatmap_matrix()"]:::viz
    end

    %% Outputs
    OF(("Output Figures<br/>(PNG/SVG)")):::entry
    OT(("Output Tables<br/>(CSV/DataFrame)")):::entry

    %% Main Flow
    CLI -->|"run_analysis.main()"| EL
    API -->|"sortscore API"| EL
    EL -->|"load_experiment_data"| DP
    DP -->|"filter_variants"| FL
    FL -->|"normalize_read_depth"| NM
    NM -->|"annotate_sequences"| AN
    AN --> SC
    SC -->|"calculate_full_activity_scores"| EX
    EX -->|"export_results"| VH
  
    VH -->|"generate_heatmap_matrix"| OF
    EX -->|"export_results"| OT

    %% Data Inputs
    Config --> EL
    RawData --> EL

    %% Click Events
    click CLI "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/run_analysis.py"
    click EL "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/load_experiment.py"
    click AN "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/annotation.py"
    click DP "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/data_processing.py"
    click FL "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/filtering.py"
    click NM "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/normalize_read_depth.py"
    click SC "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/score.py"
    click EX "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/export.py"
    click VD "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/visualization/plots.py"
    click VH "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/visualization/heatmap_matrix.py"
    click Utils "https://github.com/dbaldridge-lab/sortscore/blob/main/sortscore/analysis/utils.py"

    %% Styles
    classDef entry fill:#cccccc,stroke:#333,stroke-width:1px
    classDef pipeline fill:#bbeeff,stroke:#333,stroke-width:1px
    classDef pipelineStage fill:#bbeeff,stroke:#333,stroke-width:1px,font-size:22px
    classDef viz fill:#bbeecc,stroke:#333,stroke-width:1px
    classDef data fill:#ffeb99,stroke:#333,stroke-width:1px
    classDef ext fill:none,stroke-dasharray: 5 5,stroke:#666,stroke-width:1px
    classDef test fill:#f9d5e5,stroke:#333,stroke-width:1px

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License

MIT