FISSEQ Data Pipeline

Welcome to the FISSEQ Data Pipeline documentation.
This project provides a reproducible, configurable pipeline for processing FISSEQ cell profiling data, including cleaning, normalization, harmonization, and stratified evaluation.

Features

Command-line interface (CLI)

Access the pipeline with a single entry point:

  fisseq-data-pipeline [validate|run|configure]

For more details on command line usage see Pipeline.

Data cleaning

Remove invalid rows/columns and rare label–batch pairs. See Filter.

Normalization

Compute z-score normalization statistics on control samples and apply them across the dataset. See Normalize.

Harmonization

Apply ComBat batch correction via neuroHarmonize. See Harmonize.

Installation

This package in its current state should be considered experimental, and is thus not hosted on PyPI. However, the package may be installed directly from Github using the command:

pip install git+https://github.com/Lilferrit/fisseq-data-pipeline.git

You may also clone the repository and install dependencies:

git clone https://github.com/your-org/fisseq-data-pipeline.git
cd fisseq-data-pipeline
pip install -e .

Running the Pipeline

After installation the pipeline can be run from the command line. For more details see Pipeline.

Configuration

The pipeline may be configured using a yaml configuration file. For more details see Configuration.