GenomicRanges

Python equivalent to Bioconductor’s GenomicRanges to represent genomic locations and support genomic analysis. It uses efficient structures already available in the Pandas/NumPy eco-system.

Install

Package is deployed to PyPI

pip install genomicranges

Contents

• Overview
  • GenomicRanges
  • GenomicRangesList
  • Further information
  • Note
• Tutorial
• Construct a GenomicRanges object
  • Pandas DataFrame
  • From UCSC or GTF file
  • from IRanges (Preferred way)
  • Set sequence information
  • Get and Set methods
  • Slice operations
  • Iterate over intervals
  • Intra-range transformations
  • Inter-range methods
  • Set operations on genomic ranges
  • Compute over bins
  • Overlap based methods
  • Search operations
  • Comparison, rank and order operations
  • Combine GenomicRanges objects by rows
  • Misc operations
• Construct a GenomicRangesList object.
  • Properties
  • Combine GenomicRangeslist object
• Module Reference
  • genomicranges package
• Contributions & Help
  • Issue Reports
  • Documentation Improvements
  • Code Contributions
  • Maintainer tasks
• License
• Authors
• Changelog
  • Version 0.4.9
  • Version 0.4.0 to 0.4.8
  • Version 0.3.0
  • Version 0.2
  • Version 0.1

Indices and tables

• Index

• Module Index

• Search Page