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
• GenomicRanges: Genomic analysis
  • Installation
• Construct a GenomicRanges object
  • From Bioinformatic file formats
  • Preferred way
  • Pandas DataFrame
  • Polars DataFrame
• Sequence information
  • Getters/Setters
• Subset operations
  • Iterate over ranges
• Intra-range transformations
• Inter-range methods
• Set operations
• Compute over bins
  • Summary stats for column
  • Binned average
• Generate tiles or bins
  • Generate tiles from genome
• Coverage
• Overlap based methods
• Search operations
• Comparison, rank and order operations
• Combine GenomicRanges objects by rows
• Misc operations
• GenomicRangesList class
  • Properties
  • Combine GenomicRangeslist object
  • Empty ranges
  • Futher reading
• Module Reference
  • genomicranges package
• Contributions & Help
  • Issue Reports
  • Documentation Improvements
  • Code Contributions
  • Maintainer tasks
• License
• Authors
• Changelog
  • Version 0.5.0
  • Version 0.4.32 - 0.4.33
  • Version 0.4.27 - 0.4.31
  • Version 0.4.26
  • Version 0.4.25
  • Version 0.4.21 - 0.4.24
  • Version 0.4.20
  • Version 0.4.19
  • Version 0.4.17
  • Version 0.4.9 - 0.4.16
  • 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