pymbX 0.2.0

A Python library for downstream pipeline of 16s rRNA sequence data.

pymbX

pymbX is a Python library designed to simplify the cleaning, processing, and visualization of microbiome and metadata files. It provides a comprehensive suite of functions to handle various data manipulations, ensuring your data is ready for downstream analysis and publication-quality visualization.

Key Features

• File Validation:
  Supports common file formats including CSV, XLS, XLSX, and TXT.

• Data Cleaning & Transformation:

  • Cleans and transposes data
  • Converts data to numerical values
  • Aggregates data and calculates column-wise percentage values

• Metadata Integration:
  Merges metadata with the cleaned microbiome data seamlessly.

• Visualization:
  Generates publication-ready visualizations based on your data and specified taxonomic levels.

Library Functions

pymbX includes the following functions:

• ezclean:
  Handles the processing of microbiome and metadata files, performing robust data cleaning, transposition, aggregation, and merging operations.

• ezviz:
  Generates publication-ready visualizations using the output from ezclean. This function creates dynamic plots based on taxonomic levels and user-defined parameters.

• ezstat:
  (Upcoming Function) Designed to perform statistical analysis on 16S rRNA outputs. Stay tuned for updates!

Installation

You can install pymbX using pip:

pip install pymbX