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bio-hi-c-analysis-hic-data-io - Hi-C Data I/O and Matrix Manipulation

Load, convert, access, merge, coarsen, and export Hi-C contact matrices using cooler and hic2cool.

Tags

Updated: 2026-09-16
hi-ccoolerhic2coolgenomicsmatrixdata-io

Capabilities

Load cool and mcool filesAccess bin and pixel informationExtract contact matrices and submatricesConvert hic files to cooler

Typical Inputs

.cool and .mcool files.hic filesGenomic chromsizes and pairs data

Typical Outputs

Cooler files (.cool, .mcool)Exported matrix files (.npy, .txt, .csv)Dumped pairs and bins text files

What this skill does

  • Load cool and mcool files
  • Access bin and pixel information
  • Extract contact matrices and submatrices
  • Convert hic files to cooler
  • Create cooler files from matrices
  • Merge and coarsen cooler files
  • Export matrix data to files

Inputs

  • .cool and .mcool files
  • .hic files
  • Genomic chromsizes and pairs data
  • Contact matrix arrays

Outputs

  • Cooler files (.cool, .mcool)
  • Exported matrix files (.npy, .txt, .csv)
  • Dumped pairs and bins text files

Requirements

  • Python
  • cooler
  • hic2cool
  • numpy
  • pandas
  • bioframe
  • scipy

Source

  • Spec: SKILL.md

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