https://github.com/biocore/biom-format
The Biological Observation Matrix (BIOM) Format Project
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
13 of 57 committers (22.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Keywords from Contributors
bioinformatics
microbiome
ordination
emperor
biplots
metagenomics
sequence
genomics
usegalaxy
closember
Last synced: 10 months ago
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JSON representation
Repository
The Biological Observation Matrix (BIOM) Format Project
Basic Info
- Host: GitHub
- Owner: biocore
- License: other
- Language: Python
- Default Branch: master
- Homepage: http://biom-format.org
- Size: 20.4 MB
Statistics
- Stars: 95
- Watchers: 19
- Forks: 94
- Open Issues: 26
- Releases: 15
Created about 14 years ago
· Last pushed 10 months ago
Metadata Files
Readme
Changelog
License
README.md
The Biological Observation Matrix (BIOM) format
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing counts of observations (e.g., OTUs, KO categories, lipid types) in one or more biological samples (e.g., microbiome samples, genomes, metagenomes).
Further details can be found at http://biom-format.org.
Installation
The easiest way to install the latest version of BIOM-Format is through conda-forge:
$ conda install -c conda-forge biom-format
Alternatively, you can install the latest version through PyPI:
$ pip install biom-format
Getting help
To get help with biom, please open an issue on the Github tracker.
Owner
- Name: biocore
- Login: biocore
- Kind: organization
- Location: Cyberspace
- Website: http://biocore.github.io/
- Repositories: 76
- Profile: https://github.com/biocore
Collaboratively developed bioinformatics software.
GitHub Events
Total
- Issues event: 5
- Watch event: 3
- Issue comment event: 23
- Push event: 5
- Pull request review event: 7
- Pull request review comment event: 5
- Pull request event: 19
Last Year
- Issues event: 5
- Watch event: 3
- Issue comment event: 23
- Push event: 5
- Pull request review event: 7
- Pull request review comment event: 5
- Pull request event: 19
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel McDonald | m****t@c****u | 604 |
| Greg Caporaso | g****o@g****m | 201 |
| Jai Ram Rideout | j****t@g****m | 199 |
| Daniel McDonald | d****d@u****u | 128 |
| Jorge Cañardo Alastuey | j****o@g****m | 112 |
| Yoshiki Vázquez Baeza | y****9@g****m | 107 |
| Jose Navas | j****a@g****m | 88 |
| Adam Robbins-Pianka | a****a@c****u | 53 |
| Emily TerAvest | e****t@g****m | 53 |
| Paul J. McMurdie | m****e@s****u | 43 |
| wasade | w****e@g****m | 31 |
| Joshua Shorenstein | s****o@g****m | 15 |
| Antonio Gonzalez | a****a@g****m | 14 |
| = | e****n@g****m | 13 |
| Michael Hall | h****3@g****m | 10 |
| Morgan Langille | m****e@g****m | 8 |
| shafferm | m****r@u****u | 8 |
| Jose Carlos Clemente Litran | j****e@g****m | 5 |
| Peter Cock | p****k@g****m | 5 |
| Qiyun Zhu | q****u@g****m | 4 |
| Matt Aton | m****2@g****m | 3 |
| Nicolai Reeve | n****e@u****u | 3 |
| Luke Ursell | l****l@L****l | 2 |
| Nicola Soranzo | n****o@g****m | 2 |
| Rob Knight | r****b@r****u | 2 |
| rec3141 | r****1@g****m | 2 |
| Adam Gayoso | a****o@u****m | 1 |
| Asaf Peer | a****r@g****m | 1 |
| Ben | s****e@u****m | 1 |
| Björn Grüning | b****n@g****u | 1 |
| and 27 more... | ||
Committer Domains (Top 20 + Academic)
ucsd.edu: 3
colorado.edu: 2
stanford.edu: 1
ucdenver.edu: 1
rl1-2-205-222-dhcp.int.colorado.edu: 1
gruenings.eu: 1
4angle.com: 1
unitn.it: 1
cirad.fr: 1
colgate.edu: 1
sdsc.edu: 1
pnnl.gov: 1
umiacs.umd.edu: 1
digicat.org: 1
ufz.de: 1
posteo.net: 1
osu.edu: 1
gitter.im: 1
gcmodeller.org: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 96
- Total pull requests: 97
- Average time to close issues: 5 months
- Average time to close pull requests: 18 days
- Total issue authors: 32
- Total pull request authors: 15
- Average comments per issue: 3.27
- Average comments per pull request: 1.87
- Merged pull requests: 80
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 13
- Pull requests: 13
- Average time to close issues: about 1 month
- Average time to close pull requests: about 18 hours
- Issue authors: 4
- Pull request authors: 5
- Average comments per issue: 1.69
- Average comments per pull request: 1.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- wasade (22)
- peterjc (10)
- mortonjt (7)
- tillea (5)
- thomasstjerne (3)
- qiyunzhu (3)
- Midnighter (3)
- AmandaBirmingham (2)
- WaterKnight1998 (1)
- adamgayoso (1)
- jindongmin (1)
- arsilan324 (1)
- KasperSkytte (1)
- sandipansamaddar (1)
- UmaJan (1)
Pull Request Authors
- wasade (57)
- qiyunzhu (14)
- mataton (7)
- peterjc (7)
- sfiligoi (4)
- Midnighter (3)
- schlich (2)
- asafpr (2)
- nsoranzo (2)
- fedarko (2)
- ake123 (1)
- schferbe (1)
- mortonjt (1)
- ElDeveloper (1)
- adamgayoso (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
Packages
- Total packages: 3
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Total downloads:
- pypi 39,603 last-month
- Total docker downloads: 94,439
-
Total dependent packages: 25
(may contain duplicates) -
Total dependent repositories: 113
(may contain duplicates) - Total versions: 29
- Total maintainers: 2
pypi.org: biom-format
Biological Observation Matrix (BIOM) format
- Homepage: http://www.biom-format.org
- Documentation: https://biom-format.readthedocs.io/
- License: BSD
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Latest release: 2.1.17
published 10 months ago
Rankings
Dependent packages count: 0.9%
Docker downloads count: 1.0%
Dependent repos count: 1.5%
Average: 1.9%
Downloads: 4.0%
Maintainers (2)
Last synced:
10 months ago
conda-forge.org: biom-format
- Homepage: http://biom-format.org/
- License: BSD-3-Clause
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Latest release: 2.1.12
published about 4 years ago
Rankings
Dependent repos count: 7.8%
Dependent packages count: 10.4%
Average: 18.3%
Forks count: 19.0%
Stargazers count: 35.9%
Last synced:
10 months ago
anaconda.org: biom-format
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.
- Homepage: https://biom-format.org
- License: BSD-3-Clause
-
Latest release: 2.1.17
published 10 months ago
Rankings
Forks count: 32.6%
Average: 41.0%
Dependent packages count: 41.8%
Stargazers count: 43.5%
Dependent repos count: 46.0%
Last synced:
10 months ago
Dependencies
rtd_requirements.txt
pypi
- Sphinx ==1.2.2
setup.py
pypi
- click *
- cython *
- h5py *
- numpy *
- pandas *
- scipy *
.github/workflows/python-package-conda.yml
actions
- actions/checkout v2 composite
- actions/setup-python v2 composite
- conda-incubator/setup-miniconda v2 composite
.github/workflows/release.yml
actions
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish release/v1 composite