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. 2017 Oct 31;14(11):1023-1024.
doi: 10.1038/nmeth.4468.

Accessible, curated metagenomic data through ExperimentHub

Edoardo Pasolli  1 , Lucas Schiffer  2   3 , Paolo Manghi  1 , Audrey Renson  2   3 , Valerie Obenchain  3 , Duy Tin Truong  1 , Francesco Beghini  1 , Faizan Malik  2 , Marcel Ramos  2   3   4 , Jennifer B Dowd  2   5 , Curtis Huttenhower  6   7 , Martin Morgan  4 , Nicola Segata  1 , Levi Waldron  2   3
Affiliations

Accessible, curated metagenomic data through ExperimentHub

Edoardo Pasolli et al. Nat Methods. .
No abstract available

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Conflict of interest statement

COMPETING FINANCIAL INTERESTS

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
curatedMetagenomicData production pipeline and examples of enabled analyses. The pipeline (left) processes raw metagenomic sequence data to produce taxonomic and functional profiles, integrates these with curated sample data, then documents and packages these for distribution through ExperimentHub as the curatedMetagenomicData package. Example 1: health status was classified for six data sets, five data types each, using a random-forest algorithm and cross-validation to estimate prediction accuracy. Example 2: unsupervised clustering of human gut samples (n = 3,667) using the Bray–Curtis metric and partitioning around medoids. In Cluster 1, Bacteroides relative abundance is shown by point borders and Prevotella copri by centers. Example 3: abundance at the phylum level in human gut samples. Example 4: correlation between Prevotella copri and inosine 5 phosphate biosynthesis, the most correlated species–pathway pair (see Supplementary Fig. 4 for heatmap of most highly correlated species–pathway pairs). These analyses were performed using the script provided in the vignettes/extras package directory.
See this image and copyright information in PMC

References

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