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.
Project description
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file lefse-1.1.2.tar.gz.
File metadata
- Download URL: lefse-1.1.2.tar.gz
- Upload date:
- Size: 53.9 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.4.2 importlib_metadata/4.6.3 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.0 CPython/3.7.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 009d96ae215a922d6aefad81432a5930c8d5d1beb0092bb2a2ecdb05d25fea2f |
|
| MD5 | b9c2756b02930bb122d2c33f8c1d079a |
|
| BLAKE2b-256 | 760b21662b491ca4345b9eae6d69fc0e54ba108c91829686eaef9f109f6b88ad |
File details
Details for the file lefse-1.1.2-py3-none-any.whl.
File metadata
- Download URL: lefse-1.1.2-py3-none-any.whl
- Upload date:
- Size: 60.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.4.2 importlib_metadata/4.6.3 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.0 CPython/3.7.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 07359e212e443f5d63645ee16b3605b06fe6f7184f204e63d715a298acf683aa |
|
| MD5 | cf0fdbdf80da1a717aafedcd84065a89 |
|
| BLAKE2b-256 | b4ff0e598c1ec8f6696bc6b87df50f1e3c7b9419b5739fdab42e95bf10cfbaeb |
