Welcome to BioTK’s documentation!

Overview

BioTK is a Python toolkit, containing a library and scripts, for various bioinformatics tasks:

• Differential expression analysis on microarray and RNA-seq data
• Functional and downstream analysis of DE gene lists
• Ontology handling
• Text mining, ranging from shallow NLP to relation extraction
• Efficient storage and querying of sets of genomic intervals (similar to BEDTools, GenomicRanges, etc.)

Tutorial

• Expression analysis
  • Loading expression data
  • Normalizing expression data
  • Differential expression
  • Visualization
  • Enrichment analysis
  • Meta-analysis
• Transcript expression meta-analysis
  • Importing data
  • Performing a meta-analysis
  • Finding coexpressed genes
  • Inferring categories for genes or samples

Development information

• General development information
  • Contributors
  • License
• How to contribute
  • Writing code
    • Naming conventions
  • Documentation
    • Sphinx documentation
    • Docstrings
    • Internal code comments
  • Unit tests

Indices and tables

• Index
• Module Index
• Search Page