Data

Tools

Indexes

Applications

Experiments

Open Source Science

secimtools

A set of metabolomics tools for use in Galaxy

https://github.com/secimtools/secimtools

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    13 of 21 committers (61.9%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.0%) to scientific vocabulary

Keywords

anova galaxy lasso metabolomics pca-analysis random-forest secim
Last synced: 6 months ago · JSON representation

Repository

A set of metabolomics tools for use in Galaxy

Basic Info
  • Host: GitHub
  • Owner: secimTools
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 516 MB
Statistics
  • Stars: 11
  • Watchers: 4
  • Forks: 9
  • Open Issues: 0
  • Releases: 0
Topics
anova galaxy lasso metabolomics pca-analysis random-forest secim
Created over 10 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

Synopsis

SECIMTools project aims to develop a suite of tools for processing of metabolomics data, which can be run in a standalone mode or via Galaxy Genomics Framework.

Motivation

The SECIMTools a set of python tools that are available both as standalone and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, linear discriminant analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net).

Installation

SECIMTools are available as a secimtools pypi package. Project has also been packaged for bioconda and Galaxy Genomics Framework.

Contributors

Feel free to fork the repository and submit pull requests.

License

The project is licensed under MIT license

Owner

  • Name: SECIM
  • Login: secimTools
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,118
  • Total Committers: 21
  • Avg Commits per committer: 53.238
  • Development Distribution Score (DDS): 0.773
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
miguelib i****o@g****m 254
Jonathan p****j@u****u 223
Justin Fear j****r@u****u 213
Oleksandr Moskalenko om@r****u 188
Alison Morse a****e@u****u 39
Alison Morse a****e@u****u 37
SECIM Data Manager N****e 33
Kelsey Sinclair k****r@u****u 26
Xinlei Mi x****i@u****u 25
Kelsey Sinclair k****r@u****u 19
ZihaoLiu0927 L****7@o****m 16
Carter Johnson c****n@u****u 12
Kelsey Sinclair k****r@u****u 8
Ali Ashrafi a****i@u****u 7
Oleksandr Moskalenko om@h****u 6
Secim Admin s****m@d****c 4
Vedic Sharma v****a@u****u 4
Secim Admin s****m@g****c 1
Secim Admin s****m@g****c 1
George VanVeckhoven g****n@G****l 1
Saskia Hiltemann s****n 1
Committer Domains (Top 20 + Academic)
ufl.edu: 5 gator3.ufhpc: 1 galaxy3.ufhpc: 1 ufgi-mel.ahc.ufl.edu: 1 dev1.ufhpc: 1 hpc.ufl.edu: 1 ufgi-sim.ahc.ufl.edu: 1 ufgi-serrata.ahc.ufl.edu: 1 ufgi-vulcana.ahc.ufl.edu: 1 ufgi-suz.ahc.ufl.edu: 1 ufgi-picea.ahc.ufl.edu: 1 rc.ufl.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 2
  • Average time to close issues: 1 day
  • Average time to close pull requests: 7 months
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • 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
  • moskalenko (1)
Pull Request Authors
  • XinsongDu (1)
  • shiltemann (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 31 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: secimtools

'Metabolomics tools from the SECIM project',

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 31 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 11.4%
Stargazers count: 17.1%
Average: 19.3%
Dependent repos count: 21.7%
Downloads: 36.1%
Maintainers (1)
moskalenko
Last synced: 6 months ago

Dependencies

conda/requirements.txt pypi
  • bioconductor-impute *
  • lxml *
  • matplotlib *
  • matplotlib-venn *
  • numpy >=1.16
  • palettable *
  • pandas *
  • perl-vcftools-vcf *
  • pymc *
  • python >=3.7.3
  • r-glmnet *
  • rpy2 *
  • scikit-learn *
  • scipy *
  • seaborn *
  • statsmodels *
src/requirements.txt pypi
  • biopython >=1.77
  • biothings-client >=0.2
  • lxml >=4
  • matplotlib >=3.2.0
  • matplotlib-venn *
  • numpy >=1.18
  • palettable >=3.3.0
  • pandas >=1.0
  • patsy >=0.5
  • pymc >=2.3
  • rpy2 >=3.1
  • scikit-learn >=0.22
  • scipy >=1.4
  • seaborn >=0.10
  • statsmodels >=0.11