Package: python3-biom-format (2.1.12-3 and others)

[ Source: python-biom-format  ]

Biological Observation Matrix (BIOM) format (Python 3)

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

This package provides the BIOM format library for the Python 3 interpreter.

Other Packages Related to python3-biom-format

• dep: cython3

  C-Extensions for Python 3

• dep: libc6 (>= 2.17)

  GNU C könyvtár: megosztott könyvtárak
  also a virtual package provided by libc6-udeb

• dep: python3

  interactive high-level object-oriented language (default python3 version)

  dep: python3 (<< 3.12)

  dep: python3 (>= 3.11~)

• dep: python3-click

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• dep: python3-h5py

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• dep: python3-numpy (>= 1:1.22.0)

  Fast array facility to the Python 3 language

• dep: python3-numpy-abi9

  virtual package provided by python3-numpy

• dep: python3-pandas

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• dep: python3-scipy

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• sug: python-biom-format-doc

  documentation for BIOM format

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