Explicet published in Bioinformatics! To view the publication, click here: Explicet
Explicet version 2.10.5 released 7-21-14! For a list of new features, click here: New Features
Explicet version 2.10.5 is the final version of Explicet that will support 32 bit Windows (including Windows XP) and Mac OS 10.6 (Snow Leopard).
Welcome to Explicet
Explicet is from the Latin: explain, unfold, extend, set forth, exhibit, disentangle
Explicet is a free to use, open source software package (GPLv3) available for Windows, Mac, and Linux that facilitates the exploration and visualization of taxonomy-based microbiome datasets (a.k.a. OTU tables).
Explicet makes it easy to combine the metadata of a microbiome dataset with the taxonomic classifications of sequence data that are generated by 16S (SSU rRNA) pipelines (such as Qiime or Mothur) or by any taxonomy based tool such as RDP Classifier, ARB, or SINA.
With Explicet, it is easy to select specific samples from large datasets based on metadata criteria, such as barcode (a.k.a. Illumina index), city name, or pH value and then create graphics (pie charts, bar charts, or heatmaps). Explicet also performs statistical analyses on the data selected, such as Two-Part (which provides p-values), Morisita-Horn/Bray-Curtis/ThetaYC (classic beta diversity sample metrics), or any of the many classic alpha diversity metrics such as Shannon or Chao1: rendering the results as Manhattan plots, heatmaps, or rarefacted collector's curves.
Learn more about Explicet by clicking on the blue text below or by clicking on the tabs at the top of each page.
To get started with Explicet, it is recommended that you start with the Explicet tutorial: Getting Started with Explicet
Comprehensive documentation is available in the Explicet handbook: Explicet Documentation
The Explicet Program
The Explicet software is available (free, open source GPLv3) on the downloads page: Explicet Downloads
Questions and Answers
The authors of Explicet will be happy to address any questions via the Explicet Forum: Explicet Forum
Oft mentioned issues are addressed on the Frequently Asked Questions page: FAQ
New Features? Upcoming Releases?
Learn about the items in our software development pipeline by visiting our Coming Soon page.
Explicet is brought to you by:
Dr. Charles E. Robertson, Research Associate in The Pace Lab (Dr. Norman R. Pace, PI): Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
Dr. Daniel N. Frank, PI of The Frank Lab: Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO USA
Dr. J. Kirk Harris, PI of The Harris Lab: Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO USA
Dr. Brandie D. Wagner, Assistant Professor: Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA
All authors are members, and Drs. Frank and Harris are co-directors, of:
Our principal benefactor that made the project possible:
Mr. Bruce Holland, President of Incubix Incorporated
And the outstanding technical team at Incubix:
David, Kathy, Beth
Additional funding provided by:
- NIH grants UH2DK083994 and HG005964
- The Alfred P Sloan Foundation (Microbiology of the Built Environment: Municipal Water Systems)