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Open Source Science

https://github.com/biocore/gneiss

compositional data analysis toolbox

https://github.com/biocore/gneiss

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords

balance compositional-statistics omics tree

Keywords from Contributors

bioinformatics microbiome biplots emperor ordination
Last synced: 5 months ago · JSON representation

Repository

compositional data analysis toolbox

Basic Info
Statistics
  • Stars: 59
  • Watchers: 17
  • Forks: 27
  • Open Issues: 83
  • Releases: 0
Topics
balance compositional-statistics omics tree
Created over 9 years ago · Last pushed about 3 years ago
Metadata Files
Readme Changelog License

README.md

gneiss

Build Status Coverage Status Gitter

Canonically pronouced nice

gneiss is a compositional data analysis and visualization toolbox designed for analyzing high dimensional proportions. See here for API documentation.

Note that gneiss is not compatible with python 2, and is compatible with Python 3.4 or later. gneiss is currently in alpha. We are actively developing it, and backward-incompatible interface changes may arise.

Installation

To install this package, it is recommended to use conda. First make sure that the appropriate channels are configured.

conda config --add channels https://conda.anaconda.org/bioconda conda config --add channels https://conda.anaconda.org/biocore conda config --add channels https://conda.anaconda.org/qiime2 conda config --add channels https://conda.anaconda.org/qiime2/label/r2017.6

Then gneiss can be installed in a conda environment as follows conda create -n gneiss_env gneiss To install the most up to date version of gneiss, run the following command

pip install git+https://github.com/biocore/gneiss.git

Tutorials

Qiime2 tutorials

Python tutorials

If you use this software package in your own publications, please cite it at Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. 2017. Balance trees reveal microbial niche differentiation. mSystems 2:e00162-16. https://doi.org/10.1128/mSystems.00162-16.

Owner

  • Name: biocore
  • Login: biocore
  • Kind: organization
  • Location: Cyberspace

Collaboratively developed bioinformatics software.

GitHub Events

Total
  • Watch event: 4
Last Year
  • Watch event: 4

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 615
  • Total Committers: 5
  • Avg Commits per committer: 123.0
  • Development Distribution Score (DDS): 0.01
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jamie Morton j****n@g****m 609
Evan Bolyen e****n@g****m 3
Yoshiki Vázquez Baeza y****9@g****m 1
Lisa l****5@g****m 1
Antonio Gonzalez a****a@g****m 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 81
  • Total pull requests: 94
  • Average time to close issues: 4 months
  • Average time to close pull requests: 21 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 1.15
  • Average comments per pull request: 6.54
  • Merged pull requests: 73
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mortonjt (44)
  • tanaes (1)
Pull Request Authors
  • mortonjt (52)
  • Josh-Lefler (1)
  • gitter-badger (1)
  • wasade (1)
Top Labels
Issue Labels
high priority (5) help wanted (5) question (4) medium priority (3) wontfix (2) enhancement (2) bug (1) easy fix (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 54 last-month
  • Total docker downloads: 93,803
  • Total dependent packages: 0
  • Total dependent repositories: 7
  • Total versions: 11
  • Total maintainers: 1
pypi.org: gneiss

Compositional data analysis tools and visualizations

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 7
  • Downloads: 54 Last month
  • Docker Downloads: 93,803
Rankings
Docker downloads count: 1.1%
Dependent repos count: 5.6%
Dependent packages count: 10.0%
Average: 11.5%
Downloads: 29.2%
Maintainers (1)
mortonjt
Last synced: 6 months ago

Dependencies

ci/conda_requirements.txt pypi
  • biom-format *
  • bokeh =1.1.0
  • pip *
ci/pip_requirements.txt pypi
  • coveralls *
  • flake8 *
  • pycodestyle *
  • sphinx *
setup.py pypi
  • IPython *
  • biom-format *
  • bokeh ==1.1.0
  • matplotlib *
  • nose *
  • numpy *
  • pandas *
  • scikit-bio *
  • scipy *
  • seaborn *
  • statsmodels >=0.8.0
.github/workflows/master.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
ci/environment.yml conda
  • arrow 0.8.0
  • binaryornot 0.3.0
  • biom-format 2.1.5
  • bokeh 0.12.4
  • bz2file 0.98
  • cachecontrol 0.11.6
  • click 6.6
  • contextlib2 0.4.0
  • cookiecutter 1.4.0
  • cycler 0.10.0
  • decorator 4.0.10
  • entrypoints 0.2.2
  • flake8 2.5.1
  • freetype 2.5.5
  • future 0.15.2
  • h5py 2.6.0
  • hdf5 1.8.16
  • ijson 2.3
  • ipykernel 4.0.3
  • ipymd 0.1.2
  • ipython 3.2.3
  • ipython_genutils 0.1.0
  • ipywidgets 4.1.1
  • jinja2 2.8
  • jinja2-time 0.2.0
  • jsonschema 2.5.1
  • jupyter 1.0.0
  • jupyter_client 4.3.0
  • jupyter_console 5.0.0
  • jupyter_core 4.1.0
  • libpng 1.6.22
  • lockfile 0.12.2
  • markupsafe 0.23
  • matplotlib 1.5.1
  • mccabe 0.3.1
  • mistune 0.7.2
  • mkl 11.3.3
  • natsort 4.0.3
  • nbconvert 4.2.0
  • nbformat 4.0.1
  • nose 1.3.7
  • notebook 4.2.1
  • numexpr 2.6.1
  • numpy 1.11.2
  • openssl 1.0.2h
  • pandas 0.19.1
  • patsy 0.4.1
  • pep8 1.7.0
  • pip 8.1.2
  • poyo 0.4.0
  • prompt_toolkit 1.0.9
  • ptyprocess 0.5.1
  • pyflakes 1.2.3
  • pygments 2.1.3
  • pyparsing 2.1.4
  • pyqt 4.11.4
  • pytables 3.2.2
  • python 3.5.2
  • python-dateutil 2.5.3
  • python-frontmatter 0.2.1
  • python.app 1.2
  • pytz 2016.4
  • pyyaml 3.12
  • pyzmq 15.2.0
  • qt 4.8.7
  • qtconsole 4.0.1
  • readline 6.2
  • requests 2.10.0
  • scikit-bio 0.5.1
  • scipy 0.18.1
  • setuptools 23.0.0
  • sip 4.16.9
  • six 1.10.0
  • sqlite 3.13.0
  • statsmodels 0.8.0
  • terminado 0.6
  • tk 8.5.18
  • tornado 4.3
  • traitlets 4.2.1
  • tzlocal 1.3
  • wcwidth 0.1.7
  • wheel 0.29.0
  • whichcraft 0.4.0
  • xz 5.2.2
  • yaml 0.1.6
  • zlib 1.2.8