diff --git a/quarto/_quarto.yml b/quarto/_quarto.yml index 163bdd1..c6b3974 100755 --- a/quarto/_quarto.yml +++ b/quarto/_quarto.yml @@ -22,3 +22,4 @@ project: - dbrda.qmd - compositional_heatmap.qmd - differential_abundance.qmd + - oma.qmd diff --git a/quarto/day2_cache/revealjs/__packages b/quarto/day2_cache/revealjs/__packages deleted file mode 100755 index 34863e3..0000000 --- a/quarto/day2_cache/revealjs/__packages +++ /dev/null @@ -1,15 +0,0 @@ -matrixStats -MatrixGenerics -BiocGenerics -S4Vectors -IRanges -GenomeInfoDb -GenomicRanges -Biobase -SummarizedExperiment -SingleCellExperiment -XVector -Biostrings -TreeSummarizedExperiment -MultiAssayExperiment -mia diff --git a/quarto/oma.html b/quarto/oma.html deleted file mode 100644 index e4eee4a..0000000 --- a/quarto/oma.html +++ /dev/null @@ -1,1104 +0,0 @@ - - - - - - - - - - - - - - Orchestrating Microbiome Analysis with Bioconductor - - - - - - - - - - - - - - - - - -
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Orchestrating Microbiome Analysis with Bioconductor

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Outline

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Bioconductor sticker mia logo

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Bioconductor

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  • Community-driven open-source project
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Software

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  • Genomics, transcriptomics, microbiomics, …
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Data containers form the foundation

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SummarizedExperiment

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  • Most common data container
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  • Optimized for biological data
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- -SummarizedExperiment class
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Optimal container for microbiome data?

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Optimal container for microbiome data?

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  • Multiple assays: seamless interlinking
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Optimal container for microbiome data?

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  • Multiple assays: seamless interlinking
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  • Hierarchical data: supporting samples & features
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Optimal container for microbiome data?

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Optimal container for microbiome data?

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  • Optimized: for speed & memory
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Optimal container for microbiome data?

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Optimal container for microbiome data?

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  • Optimized: for speed & memory
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Reduce overlapping efforts, improve interoperability, ensure sustainability.

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TreeSummarizedExperiment

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  • Extension to SummarizedExperiment
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  • Optimal for microbiome data
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  • Allows us to develop modular and efficient workflows
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MIcrobiome Analysis (mia)

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  • Microbiome data science in SummarizedExperiment ecosystem
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  • mia package top 7.6% Bioconductor downloads
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mia ecosystem

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Advantages

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  • Shared data container
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  • Scalable & optimized for large datasets
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# Load package
-library(mia)
-# Load example dataset
-data("peerj13075")
-tse <- peerj13075
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class: TreeSummarizedExperiment 
-dim: 674 58 
-metadata(0):
-assays(1): counts
-rownames(674): OTU1 OTU2 ... OTU2567 OTU2569
-rowData names(6): kingdom phylum ... family genus
-colnames(58): ID1 ID2 ... ID57 ID58
-colData names(5): Sample Geographical_location Gender Age Diet
-reducedDimNames(0):
-mainExpName: NULL
-altExpNames(0):
-rowLinks: NULL
-rowTree: NULL
-colLinks: NULL
-colTree: NULL
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# Agglomerate to genus level
-tse <- agglomerateByRank(tse, rank = "genus")
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# Agglomerate to genus level
-tse <- agglomerateByRank(tse, rank = "genus")
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-# Add relative abundances
-tse <- transformAssay(tse, method = "relabundance")
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# Load visualization package
-library(miaViz)
-# Summarize abundance of top taxa
-plotAbundanceDensity(tse, assay.type = "relabundance")
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# Calculate alpha diversity indices
-tse <- addAlpha(tse, index = "shannon")
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# Calculate alpha diversity indices
-tse <- addAlpha(tse, index = "shannon")
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-# Load single-cell analysis package that has useful, complementary tools
-library(scater)
-# Plot alpha diversity
-plotColData(tse, x = "Geographical_location", y = "shannon")
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# Perform PCoA
-tse <- runMDS(tse, assay.type = "relabundance", FUN = getDissimilarity, method = "bray")
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# Perform PCoA
-tse <- runMDS(tse, assay.type = "relabundance", FUN = getDissimilarity, method = "bray")
-# Plot PCoA
-plotReducedDim(tse, dimred = "MDS", colour_by = "Geographical_location")
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Orchestrating Microbiome Analysis with Bioconductor

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  • Resources and tutorials for microbiome analysis
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  • Community-built best practices
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  • Open to contributions!
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Go to the book

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microbiome.github.io/OMA

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Thank you for your time!

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Moreno-Indias et al. (2021)

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University of Turku logo UTU logo Research Council of Finland logo

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https://microbiome.github.io/

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