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lefse

https://github.com/segatalab/lefse

Science Score: 20.0%

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
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 12 committers (8.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.6%) to scientific vocabulary

Keywords from Contributors

biobakery metagenomics public
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: SegataLab
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 264 KB
Statistics
  • Stars: 85
  • Watchers: 2
  • Forks: 48
  • Open Issues: 25
  • Releases: 0
Created over 6 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

LEfSe

LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.

LEfSe is available as a Galaxy module, a Conda formula, a Docker image, and included in bioBakery (VM and cloud). For additional information, please refer to the LEfSe paper.

Installation

LEfSe can be installed with Conda or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install LEfSe because the tool and its dependencies are already installed.

Install with Conda: $ conda install -c bioconda lefse

Install with Docker: $ docker run -it biobakery/lefse bash

LEfSe requires R v. 3.6 or higher and the R libraries survival, mvtnorm, modeltools, coin, MASS.

We provide support for LEfSe users. Please join our bioBakery Support Forum designated specifically for LEfSe users.

Owner

  • Name: Segata Lab
  • Login: SegataLab
  • Kind: organization
  • Location: Trento

The computational metagenomics lab at the Dep. CIBIO, University of Trento

GitHub Events

Total
  • Issues event: 3
  • Watch event: 8
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 8
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 78
  • Total Committers: 12
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.667
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nicola Segata n****a@u****t 26
Francesco Beghini f****i@u****t 18
ljmciver l****r@g****m 11
Constantino Schillebeeckx c****o@m****m 7
Francesco Asnicar f****r@u****t 4
chentong c****y@1****m 3
George_Weingart G****t@l****t 2
geno.gr g****r@g****m 2
fasnicar f****r@g****m 2
Vic_ks s****0@h****m 1
Daniel Blankenberg d****n@b****u 1
Hirun H****n 1
Committer Domains (Top 20 + Academic)
unitn.it: 3 bx.psu.edu: 1 163.com: 1 matatu.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 29
  • Total pull requests: 5
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 25 days
  • Total issue authors: 27
  • Total pull request authors: 4
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.6
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • glucksfall (2)
  • lauramason326 (2)
  • Yuxia88 (1)
  • marwa38 (1)
  • wolvesled (1)
  • Hoeferlin (1)
  • huangziyan11111 (1)
  • nttg8100 (1)
  • jwframe28 (1)
  • rpelicae (1)
  • LianheCai078 (1)
  • liu-congcong (1)
  • UmaJan (1)
  • DrKADunn (1)
  • chlige (1)
Pull Request Authors
  • Tong-Chen (2)
  • Hirun (1)
  • sagun98 (1)
  • ljmciver (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 87 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: lefse

LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 87 Last month
Rankings
Forks count: 6.2%
Stargazers count: 8.6%
Dependent packages count: 10.0%
Average: 13.8%
Dependent repos count: 21.7%
Downloads: 22.4%
Maintainers (1)
biobakery
Last synced: 11 months ago

Dependencies

setup.py pypi
  • numpy *