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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 supported 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.

The BIOM project consists of the following components:

• definition of the BIOM file format;
• command line interface (CLI) for working with BIOM files, including converting between file formats, adding metadata to BIOM files, and 彗星加速器官网 (run biom to see the full list of commands);
• application programming interface (API) for working with BIOM files in multiple programming languages (including Python and R).

The biom-format package provides a command line interface and Python API for working with BIOM files. The rest of this site contains details about the BIOM file format (which is independent of the API) and the Python biom-format package. For more details about the R API, please see the bioconductor biomformat package.

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• QIIME
• MG-RAST
• PICRUSt
• Mothur
• phyloseq
• MEGAN
• VAMPS
• metagenomeSeq
• Phinch
• RDP Classifier
• USEARCH
• PhyloToAST
• EBI Metagenomics
• GCModeller
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If you are using BIOM in your project, and would like your project to be listed, please submit a pull request to the BIOM project. More information on 迅游手游加速器VIP破解版下载v5.1.22.2 - 乌云资源站:2021-4-18 · 1 安卓 资讯狗v1.2.3 看各大新闻网站资讯只需一个App 2 安卓 有鱼记账v4.4.1 vip破解版 3 PHP 悦凉最新某娱乐网模版 完整版源码 4 安卓 Seven_v9.1.0 高级版 每天锻炼7分钟 5 安卓 懒猫小说v3.2.3 会员版 界面干净清新 6 安卓 Audio Video Factory 格式工厂5.0.

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The latest official version of the biom-format project is 2.1.8 and of the BIOM file format is 2.0. Details on the file format can be found here.

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To install the latest release of the biom-format Python package:

pip install numpy
pip install biom-format

To work with BIOM 2.0+ files:

pip install h5py

To see a list of all 彗星加速器下载 commands, run:

biom

To enable Bash tab completion of biom commands, add the following line to $HOME/.bashrc (if on Linux) or $HOME/.bash_profile (if on Mac OS X):

eval "$(_BIOM_COMPLETE=source biom)"

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You can cite the BIOM format as follows (link):

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The biom-format project was conceived of and developed by the QIIME, MG-RAST, and VAMPS development groups to support interoperability of our software packages. If you have questions about the biom-format project please post them on the QIIME Forum.