Science Score: 59.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
1 of 11 committers (9.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
R implementation of the LEfSe method
Basic Info
- Host: GitHub
- Owner: waldronlab
- Language: R
- Default Branch: devel
- Homepage: https://waldronlab.io/lefser/
- Size: 18.6 MB
Statistics
- Stars: 58
- Watchers: 8
- Forks: 5
- Open Issues: 9
- Releases: 0
Topics
Metadata Files
README.md
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lefser: Run LEfSe in R
lefser is the R implementation of the Python package, Linear discriminant analysis (LDA) Effect Size (LEfSe). LEfSe is the most widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization (Segata et al. 2011). LEfSe utilizes standard statistical significance tests along with supplementary tests that incorporate biological consistency and the relevance of effects to identity the features (e.g., organisms, clades, OTU, genes, or functions) that are most likely to account for differences between the two sample classes of interest, referred as ‘classes’. While LEfSe is widely used and available in different platform such as Galaxy UI and Conda, there is no convenient way to incorporate it in R-based workflows. Thus, we re-implement LEfSe as an R/Bioconductor package, lefser. Following the LEfSe‘s algorithm including Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis, with some modifications, lefser successfully reproduces and improves the original statistical method and the associated plotting functionality.
Citation
If you use lefser in published research, please cite:
Asya Khleborodova, Samuel D Gamboa-Tuz, Marcel Ramos, Nicola Segata, Levi Waldron, Sehyun Oh, Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R, Bioinformatics, 2024;, btae707, doi:10.1093/bioinformatics/btae707
A BibTeX entry for LaTeX users is:
@article{10.1093/bioinformatics/btae707,
author = {Khleborodova, Asya and Gamboa-Tuz, Samuel D and Ramos, Marcel and Segata, Nicola and Waldron, Levi and Oh, Sehyun},
title = {Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R},
journal = {Bioinformatics},
pages = {btae707},
year = {2024},
month = {11},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btae707},
url = {https://doi.org/10.1093/bioinformatics/btae707},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae707/60811200/btae707.pdf},
}
Owner
- Name: Waldron Lab at the CUNY SPH
- Login: waldronlab
- Kind: organization
- Email: Levi.Waldron@sph.cuny.edu
- Location: New York, NY, USA
- Website: https://waldronlab.io/
- Twitter: LeviWaldron1
- Repositories: 93
- Profile: https://github.com/waldronlab
Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City
GitHub Events
Total
- Issues event: 11
- Watch event: 16
- Delete event: 6
- Issue comment event: 10
- Push event: 27
- Pull request review comment event: 3
- Pull request review event: 5
- Pull request event: 7
- Fork event: 1
- Create event: 9
Last Year
- Issues event: 11
- Watch event: 16
- Delete event: 6
- Issue comment event: 10
- Push event: 27
- Pull request review comment event: 3
- Pull request review event: 5
- Pull request event: 7
- Fork event: 1
- Create event: 9
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Asya | a****b@g****m | 52 |
| Levi Waldron | l****h@g****m | 39 |
| LiNk-NY | m****9@g****m | 23 |
| LiNk-NY | m****z@r****g | 21 |
| LiNk-NY | m****s@r****g | 14 |
| Nitesh Turaga | n****a@g****m | 8 |
| J Wokaty | j****y@s****u | 4 |
| J Wokaty | j****y | 2 |
| Marcel Ramos | L****Y | 2 |
| Asya Khleborodova | a****a@A****l | 1 |
| Caffery Yang | c****0@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 48
- Total pull requests: 32
- Average time to close issues: 11 months
- Average time to close pull requests: 16 days
- Total issue authors: 21
- Total pull request authors: 8
- Average comments per issue: 2.15
- Average comments per pull request: 1.44
- Merged pull requests: 27
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 15
- Pull requests: 12
- Average time to close issues: 12 days
- Average time to close pull requests: 3 days
- Issue authors: 7
- Pull request authors: 4
- Average comments per issue: 1.27
- Average comments per pull request: 1.83
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lwaldron (16)
- shbrief (11)
- sdgamboa (3)
- LiNk-NY (3)
- asyakhl (2)
- morganx (1)
- dannynielsen0 (1)
- CarolineWasen (1)
- J5886 (1)
- Hesham999666 (1)
- jdaledge (1)
- susheelbhanu (1)
- anapopov (1)
- agatadziegiel (1)
- yasir-binfo (1)
Pull Request Authors
- LiNk-NY (16)
- sdgamboa (16)
- asyakhl (9)
- lwaldron (6)
- shbrief (2)
- Peacesandy (1)
- jwokaty (1)
- cafferychen777 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 35,088 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: lefser
R implementation of the LEfSE method for microbiome biomarker discovery
- Homepage: https://github.com/waldronlab/lefser
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/lefser/inst/doc/lefser.pdf
- License: Artistic-2.0
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Latest release: 1.18.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- JamesIves/github-pages-deploy-action v4 composite
- actions/cache v2 composite
- actions/checkout v3 composite
- R >= 4.0.0 depends
- SummarizedExperiment * depends
- MASS * imports
- S4Vectors * imports
- coin * imports
- ggplot2 * imports
- methods * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- covr * suggests
- curatedMetagenomicData * suggests
- knitr * suggests
- phyloseq * suggests
- pkgdown * suggests
- rmarkdown * suggests
- testthat * suggests
- withr * suggests