FISSEQ Data Pipeline

Welcome to the FISSEQ Data Pipeline documentation.

Features

Command-line interface (CLI)

Access the pipeline with a single entry point:

  fisseq-data-pipeline [run|configure]

For more details on command line usage see Pipeline.

Data cleaning

Remove invalid rows and columns — specifically columns that contain all NaN values, followed by rows that contain any remaining NaN values.

See Filter.

Normalization

Compute z-score normalization statistics on control samples and apply them across the dataset. By default z-score normalization is fit only to control samples. Fitting only to control samples ensures that biological variation is captured even in the case where biological covariants are largely disjoint across batches.

See Normalize.

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.