bja_utils

bja_utils is a Python package providing convenience functions for mass spectrometry proteomics and lipidomics analysis, data parsing, statistics, biological interpretation, and plotting. The methods streamline common tasks in Python pipelines for omics researchers.

Installation

You can install the latest release via PyPI:

pip install bja_utils

Features

• Data processing and transformation
• Statistical analysis functions
• Visualization and plotting utilities
• Parsing tools for common data formats
• Biological interpretation helpers

Package Structure

The package is organized into the following modules:

analysis

Statistical functions and models for downstream analysis. Supports descriptive statistics, hypothesis testing, regression models, and more.

processing

Functions for data preprocessing, multi-processing of computationally intensive tasks, normalization, imputation, and cleaning. Includes tools for handling missing values, scaling, and aggregating omics data.

plotting

Helper functions for common plotting tasks matplotlib and plotly. Simplifies custom styling, multi-panel figures, and specialized omics visualizations.

utils

General helper functions for file handling, logging, and other repetitive tasks that don’t fit into other modules.

Optional modules

Install all optional modules with pip install bja_utils[all].

plotly_apps

Classes for specialized omics visualizations using plotly. Install with pip install bja_utils[plotly_apps].

parsing

Functions for reading, parsing, and converting glycoproteomics and lipidomics identifiers. Install with pip install bja_utils[parsing].