EigenMS

EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence.

Please download EigenMS.zip file (latest version).

Latest version uploaded in October 2017 has a bugfix for single treatment group normalization.
Rescaling has been omitted from 2015.

EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be utilized for any -omic platform.

We have shown its utility in LC-MS/MS and metabolomics in the following two papers:

1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition".
Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR.
Bioinformatics 2009

2) "Metabolomics data normalization with EigenMS"
Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM.
PLoS One 2014

Project Activity

See All Activity >

License

GNU General Public License version 2.0 (GPLv2), GNU General Public License version 3.0 (GPLv3)

Follow EigenMS

EigenMS Web Site

Other Useful Business Software

Zenflow- The AI Workflow Engine for Software Devs

Parallel agents. Multi-agent orchestration. Specs that turn into shipped code. Zenflow automates planning, coding, testing, and verification.

Zenflow is the AI workflow engine built for real teams. Parallel agents plan, code, test, and verify in one workflow. With spec-driven development and deep context, Zenflow turns requirements into production-ready output so teams ship faster and stay in flow.

Try free now

Rate This Project

User Reviews

Be the first to post a review of EigenMS!

Additional Project Details

Intended Audience

Science/Research

Programming Language

MATLAB, S/R

Related Categories

MATLAB Bio-Informatics Software, S/R Bio-Informatics Software

Registered

2009-01-18

Similar Business Software

Bioconductor

The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. Resources to maximize the potential of Bioconductor. From basic functionalities to...

See Software
MEGA

MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis...

See Software
Galaxy

Galaxy is an open source, web-based platform for data-intensive biomedical research. If you are new to Galaxy start here or consult our help resources. You can install your own Galaxy by following the tutorial and choosing from thousands of tools from the tool shed. This instance of Galaxy is...

See Software
BioTuring Browser

Explore hundreds of curated single-cell transcriptome datasets, along with your own data, through interactive visualizations and analytics. The software also supports multimodal omics, CITE-seq, TCR-seq, and spatial transcriptomic. Interactively explore the world's largest single-cell expression...

See Software
OmicsBox

OmicsBox is a leading bioinformatics solution that offers end-to-end data analysis of genomes, transcriptomes, metagenomes, and genetic variation studies. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex...

See Software
G6GFINDR System

g6gTech, Inc. is a software development company that creates in-depth search products in the bioinformatics and artificial intelligence (AI) fields. We have recently changed our name from the G6G Consulting Group to emphasize our focus on creating products. Powered by semantic annotation, the...

See Software