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Summary of features
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- Configuring METAREP
- How to Contribute to METAREP
- Index Replication and Load Balancing
- Installation Guide v 1.2.0
- Installation Guide v 1.3.0
- Installation guide v 1.3.1
- Installation guide v 1.3.2
- Installation Guide v 1.4.0
- Summary of features
- Under the hood the METAREP search engine
- Update Taxonomy and Pathway Information
- Virtual Machine Installation Guide
- What METAREP Is
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- Handle extremely large datasets. Uses scalable high-performance Solr/Lucene search engine (we have indexed 300 million annotation entries, but much larger volumes can be handled as shown by Hathi Trust).
Compare 20+ datasets at the same time. Use various compare
options including statistical tests and plot options to visualize
dataset difference at various taxonomic and functional levels.
Apply statistical tests such as METASTATS (White et al.), a modified
non-parametric t-test to compare two sample populations (e.g.
metagenomics samples from healthy and diseased individuals).
- Export publication-ready graphics. Export heatmaps, hierarchical clustering, and multi-dimensional scaling plots in PDF format.
Analyze KEGG metabolic pathways. Summaries include enzyme
highlights on KEGG maps, pathway enzyme distributions, and
statistics about pathway coverage at various pathway levels.
Search using a SQL-like query syntax. Build your query using 14
different fields that can be combined logically.
Drill down into data using METAREP’s NCBI Taxonomy, Gene
Ontology, Enzyme Classification or KEGG Pathway browser.
Install your own METAREP version.
- Flexible central configuration, METAREP and 3rd party code base is completely open source.
Cross-link function with phylogeny. Slice your data at various
taxonomic and/or functional levels. For example, search for all
bacteria or exclude eukaryotes or search for a certain (GO/EC
Generic data format. Data types that can be populated include a
free text functional description, best BLAST hit information, as well
as GO ID, EC ID, and HMMs.