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# Anomaly pipeline
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# rANOMALY
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This amplicon sequencing analysis workflow is fully written in R. It is based on [Dada2](https://pubmed.ncbi.nlm.nih.gov/27214047/) amplicon sequence variants to reveal microbial communities and [Phyloseq](https://joey711.github.io/phyloseq/index.html) R objects to handle datas.
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... | ... | @@ -10,21 +10,20 @@ rANOMALY improvements: |
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- Alpha and beta diversity indexes are compared between conditions with integrated statistical analysis (ANOVA, permanova and non-parametric test).
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- Three main differential analysis methods ([DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html), [Metacoder](https://grunwaldlab.github.io/metacoder_documentation/), [metagenomeSeq](https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html)) are integrated to decipher differences between communities composition.
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## Test datasets
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rANOMALY is full described in the publication:
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Datasets to reproduce the use cases are available at this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM)
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## Databases
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We share all the databases we currently use for IDTAXA in this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM).
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Sebastien Theil and Etienne Rifa. « RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis ». F1000Research 10 (07/01/2021): 7. https://doi.org/10.12688/f1000research.27268.1.
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## [Install procedure](install)
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## [Install](install)
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## [IDTAXA formatting database procedure](idtaxa_db_proc)
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## Use Case
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A fully documented use case is available [HERE](https://umrf.pages.mia.inra.fr/ranomaly/use_case.html)
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Datasets to reproduce the use case are available at this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM)
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## Databases
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## [idtaxa formatting database procedure](idtaxa_db_proc) |
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We share all the databases we currently use for IDTAXA in this [link](https://nextcloud.inrae.fr/s/Zx3iASe64x8oSoM). |