https://github.com/biocore/deicode

Robust Aitchison PCA from sparse count data

Science Score: 10.0%

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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Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
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Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary

Keywords from Contributors

microbiome bioinformatics biplots qiime qiime2

Last synced: 9 months ago · JSON representation

Repository

Robust Aitchison PCA from sparse count data

Basic Info

Host: GitHub
Owner: biocore
License: other
Language: JavaScript
Default Branch: master
Homepage:
Size: 434 MB

Statistics

Stars: 34
Watchers: 6
Forks: 17
Open Issues: 15
Releases: 0

Created over 9 years ago · Last pushed almost 4 years ago

Metadata Files

Readme Changelog License

README.md

DEICODE is a tool box for running Robust Aitchison PCA on sparse compositional omics datasets, linking specific features to beta-diversity ordination.

UPDATE

All future development on Robust Aitchison PCA has been moved from this repository to Gemelli. The code in this respository will be maintained for the current functionality. Merging to Gemelli allows for the matrix and tensor based methods to be accessed in the same location, since they share some functionality.

Installation

To install the most up to date version of deicode, run the following command

# pip (only supported for QIIME2 >= 2018.8)
pip install deicode

# conda (only supported for QIIME2 >= 2019.1)
conda install -c conda-forge deicode

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

Using DEICODE inside QIIME 2

The QIIME2 forum tutorial can be found here.
The official plugin docs and tutorial can be found here.
The in-repo tutorial can be found here.

Using DEICODE as a standalone tool

There are two commands within deicode. The first is rpca and the second is auto-rpca. The only difference is that auto-rpca automatically estimates the underlying-rank of the matrix and requires no input for the n_components parameter. In the rpca the n_components must be set explicitly. The structure of the commands follows the QIIME2 commands exactly and so questions about the use of the tool can be answered in the tutorial in the Using DEICODE inside QIIME 2 section above. However, an example analysis without the use of QIIME2 can be found here.

Using DEICODE as a Python API

The rpca functionality of DEICODE is also exposed as a python API. An example analysis without the use of the command line can be found here.

Other Resources

Aitchison Distance Introduction
The code for OptSpace was translated to python from a MATLAB package maintained by Sewoong Oh (UIUC).
Transforms and PCoA : Scikit-bio
Data For Examples : Qiita

Simulation and Benchmarking

simulations and case studies

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

Watch event: 3

Last Year

Watch event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 566
Total Committers: 8
Avg Commits per committer: 70.75
Development Distribution Score (DDS): 0.258

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Cameron Martino	c**o@g**m	420
cameron martino	c**o@c**l	50
Marcus Fedarko	m**o@u**u	39
Jamie Morton	j**n@g**m	31
cameron martino	c**o@c**l	18
cameron martino	c**n@a**m	6
Justin Shaffer	j**r@g**m	1
Lisa	l**5@g**m	1

Committer Domains (Top 20 + Academic)

ascusbiosciences.com: 1 ucsd.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time

Total issues: 34
Total pull requests: 34
Average time to close issues: 17 days
Average time to close pull requests: 4 days
Total issue authors: 16
Total pull request authors: 7
Average comments per issue: 2.35
Average comments per pull request: 2.15
Merged pull requests: 29
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: 2 days
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 0.67
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

cameronmartino (10)
Jigyasa3 (6)
mortonjt (4)
jolespin (2)
erfanshekarriz (1)
magibc (1)
mestaki (1)
fedarko (1)
manasson (1)
gwarmstrong (1)
Hesham999666 (1)
justinshaffer (1)
scleractinia (1)
nvpatin (1)
scher-lab (1)

Pull Request Authors

cameronmartino (18)
mortonjt (9)
fedarko (3)
lisa55asil (1)
justinshaffer (1)
davised (1)
fossabot (1)

Top Labels

Issue Labels

enhancement (8) bug (3)

Pull Request Labels

enhancement (3) bug (1)

Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 8

conda-forge.org: deicode

Homepage: https://github.com/biocore/DEICODE
License: BSD-3-Clause
Latest release: 0.2.4
published over 6 years ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Forks count: 36.1%

Average: 40.7%

Stargazers count: 41.4%

Dependent packages count: 51.2%

Last synced: 10 months ago

Dependencies

ci/conda_requirements.txt pypi

IPython >4.0.0
biom-format *
flake8 *
matplotlib *
nose *
notebook *
numpy >=1.12.1
pandas *
pep8 *
pip *
scikit-bio *
scikit-learn *
scipy *
seaborn *

ci/pip_requirements.txt pypi

coveralls *
gneiss *

setup.py pypi

biom-format *
click *
h5py *
nose *
numpy *
pandas *
scikit-bio *
scipy *