SummarizedExperiment

This package provides containers to represent genomic experimental data as 2-dimensional matrices, follows Bioconductor’s SummarizedExperiment. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent samples or cells.

The package currently includes representations for both SummarizedExperiment and RangedSummarizedExperiment. A distinction lies in the fact RangedSummarizedExperiment object provides an additional slot to store genomic regions for each feature and is expected to be GenomicRanges (more here).

Install

To get started, Install the package from PyPI,

pip install summarizedexperiment

Contents

• Overview
  • Construct a SummarizedExperiment object
  • Delayed or file-backed arrays
  • Interop with anndata
  • Getters/Setters
  • Subset experiments
  • Combining experiments
• Extending Classes
  • Define the new class
  • Add a new slot or attribute
  • Define getters/setters
  • Define shallow and deep copy methods
  • Subset operation
  • Putting it all together
• Module Reference
  • summarizedexperiment package
• Contributions & Help
  • Issue Reports
  • Documentation Improvements
  • Code Contributions
  • Maintainer tasks
• License
• Authors
• Changelog
  • Version 0.5.0
  • Version 0.4.2 - 0.4.5
  • Version 0.4.0 to 0.4.1
  • Version 0.3.0
  • Version 0.1.4
  • Version 0.1.3
  • Version 0.1.2
  • Version 0.1.1
  • Version 0.1

Indices and tables

• Index

• Module Index

• Search Page