{"categories":[{"label":"Python Modules","url":"https://skillfed.io/packages/category/software-development-libraries-python-modules/18"},{"label":"Application Frameworks","url":"https://skillfed.io/packages/category/software-development-libraries-application-frameworks/5"},{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"}],"enrichment":{"capability":"Reads, writes, and manipulates Biological Observation Matrix (BIOM) files, a standard format for storing counts of observations across biological samples.","skillfed_tags":["bioinformatics","microbiome","data-format"],"use_cases":["Load and parse BIOM files from microbiome pipelines for downstream statistical analysis.","Convert between BIOM and tabular formats for integration with other analysis tools.","Manipulate sample metadata and observation taxonomy within a BIOM matrix programmatically.","Export abundance tables from your own analysis pipeline in the standard BIOM format.","Batch process multiple BIOM files to extract subsets of samples or observations."],"what_it_does":"biom-format is a Python library for working with the BIOM (Biological Observation Matrix) file format, a standard in microbiome and metagenomic research for storing abundance data\u2014counts of observations such as OTUs, KO categories, or lipid types across multiple biological samples. It provides read/write access to BIOM files, typically in HDF5 format, and allows you to load, manipulate, and export these matrices for downstream analysis.\n\nThe package depends on numpy, scipy, pandas, h5py, and click, making it suitable for integration into data pipelines. It supports Python 3.9 through 3.13 on major platforms. The library is designed to be a general-purpose container for observation counts from various high-throughput biological assays.","worth_installing":"Yes, if you work with microbiome or metagenomic data in BIOM format. The package is stable, permissively licensed, and widely compatible across platforms and Python versions. However, maintenance is aging (last release 353 days ago), so verify that it meets your specific pipeline requirements before committing to it for production workflows. No known security vulnerabilities."},"id":"biom-format","links":{"html":"https://skillfed.io/packages/biom-format","md":"https://skillfed.io/packages/biom-format.md","pypi":"https://pypi.org/project/biom-format/"},"maintenance":{"status":"aging"},"meta":{"latest_release":"2025-08-26","license_spdx":null,"license_treatment":"permissive","name":"biom-format","python_support":"supports_current","summary":"Biological Observation Matrix (BIOM) format"},"popularity":{"monthly_downloads":134204,"position":11483,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"2.1.17"}