Add MgnifyR slides

microbiome · Sep 21, 2024 · 0c42adf · 0c42adf
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diff --git a/docs/images/BioconductorSticker1.png b/docs/images/BioconductorSticker1.png
diff --git a/docs/images/ENA-logo.png b/docs/images/ENA-logo.png
diff --git a/docs/images/mgnify_logo.png b/docs/images/mgnify_logo.png
diff --git a/docs/images/mgnifyr_logo.png b/docs/images/mgnifyr_logo.png
diff --git a/docs/mgnifyr.html b/docs/mgnifyr.html
diff --git a/docs/search.json b/docs/search.json
@@ -1566,5 +1566,54 @@
     "title": "Tabular data analysis",
     "section": "",
     "text": "Data: SummarizedExperiment: rowData, colData, assays\nMethods: subsetting, transformations"
+  },
+  {
+    "objectID": "mgnifyr.html#contents",
+    "href": "mgnifyr.html#contents",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "Contents",
+    "text": "Contents\n\nIntroduction to MGnify\nOverview of MGnifyR\nBioconductor and MGnifyR"
+  },
+  {
+    "objectID": "mgnifyr.html#mgnify",
+    "href": "mgnifyr.html#mgnify",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "MGnify",
+    "text": "MGnify\n\nMicrobiome database hosted by EMBL/EBI\nRaw sequences from ENA\nStandardized bioinformatics pipelines"
+  },
+  {
+    "objectID": "mgnifyr.html#data-availability",
+    "href": "mgnifyr.html#data-availability",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "Data availability",
+    "text": "Data availability\n\nOpen access\nTaxonomy and functional mappings along with genome catalogues\nApplication Programming Interface (API)"
+  },
+  {
+    "objectID": "mgnifyr.html#problem-in-api",
+    "href": "mgnifyr.html#problem-in-api",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "Problem in API",
+    "text": "Problem in API\n\nRequires familiarity with API workflows, database structures, and linkages.\nLeads to challenges in reproducibility and time-consuming data wrangling."
+  },
+  {
+    "objectID": "mgnifyr.html#mgnifyr",
+    "href": "mgnifyr.html#mgnifyr",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "MGnifyR",
+    "text": "MGnifyR\n\nR/Bioconductor package\nStreamlines access to MGnify database\nBridges the gap between data resources and tools"
+  },
+  {
+    "objectID": "mgnifyr.html#functions",
+    "href": "mgnifyr.html#functions",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "Functions",
+    "text": "Functions\n\nMgnifyClient(): Constructor for MgnifyClient object.\ndoQuery(): Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.\nsearchAnalysis(): Look up analysis accession IDs for one or more study or sample accessions.\ngetMetadata(): Get all study, sample and analysis metadata for the supplied analysis accessions.\ngetResult(): Get microbial and/or functional profiling data for a list of accessions.\ngetData(): Versatile function to retrieve raw results.\ngetFile() & searchFile(): Download any MGnify files, also including processed reads and identified protein sequences."
+  },
+  {
+    "objectID": "mgnifyr.html#bioconductor-and-mgnifyr",
+    "href": "mgnifyr.html#bioconductor-and-mgnifyr",
+    "title": "MGnifyR: An R package for accessing MGnify microbiome data",
+    "section": "Bioconductor and MGnifyR",
+    "text": "Bioconductor and MGnifyR\n\nMicrobial and functional profiling data is retrieved as TreeSE/MAE format.\nCommon data format supported broadly by Bioconductor.\nEnables direct access to cutting-edge tools (e.g. miaverse)."
   }
 ]
diff --git a/quarto/_quarto.yml b/quarto/_quarto.yml
@@ -9,6 +9,7 @@ project:
     - bioconductor.qmd
     - starting.qmd
     - reproducible_workflow.qmd
+    - mgnifyr.qmd
     - datacontainers.qmd
     - data_manipulation.qmd    
     - summarizedexperiment.qmd

diff --git a/quarto/images/BioconductorSticker1.png b/quarto/images/BioconductorSticker1.png
diff --git a/quarto/images/ENA-logo.png b/quarto/images/ENA-logo.png
diff --git a/quarto/images/mgnify_logo.png b/quarto/images/mgnify_logo.png
diff --git a/quarto/images/mgnifyr_logo.png b/quarto/images/mgnifyr_logo.png
diff --git a/quarto/index.qmd b/quarto/index.qmd
@@ -19,6 +19,10 @@ This website hosts quarto presentations about microbiome analysis and data integ
 -   [Learning environment](https://microbiome.github.io/outreach/starting.html){target="_blank"}
 -   [Workflow](https://microbiome.github.io/outreach/workflow.html){target="_blank"}
 
+### Packages
+
+- [MGnifyR: An R package for accessing MGnify microbiome data](https://microbiome.github.io/outreach/mgnifyr.html)
+
 ### Data containers
 
 -   [Orchestrating microbiome multi-omics with R & Bioconductor](https://microbiome.github.io/outreach/lahti_bioc2023.html){target="_blank"}
@@ -54,7 +58,7 @@ The following is a quick workflow for contributions:
 
 3.  update the [\_quarto.yml file](https://github.com/microbiome/outreach/blob/main/quarto/_quarto.yml) and the list of presentations in the [website](https://github.com/microbiome/outreach/blob/main/quarto/index.qmd) with the name of the qmd file(s) with your presentation(s)
 
-4.  run `quarto render`, or in R `quarto::render(myfilename)` from your terminal from within the quarto sub-directory
+4.  run `quarto render`, or in R `quarto::quarto_render(myfilename)` from your terminal from within the quarto sub-directory
 
 5.  and make a pull request to the master branch
 

diff --git a/quarto/mgnifyr.qmd b/quarto/mgnifyr.qmd
@@ -0,0 +1,58 @@
+---
+title: "MGnifyR: An R package for accessing MGnify microbiome data"
+format: revealjs
+editor: visual
+---
+
+## Contents
+
+1. Introduction to MGnify
+2. Overview of `MGnifyR`
+3. Bioconductor and `MGnifyR`
+
+## MGnify
+
+- [Microbiome database hosted by EMBL/EBI](https://www.ebi.ac.uk/metagenomics)
+- Raw sequences from [ENA](https://www.ebi.ac.uk/ena/browser/home)
+- Standardized bioinformatics pipelines
+
+![](images/mgnify_logo.png){width="250" style="margin-right: 30px;"}
+![](images/ENA-logo.png){width="250"}
+
+## Data availability
+
+- Open access
+- Taxonomy and functional mappings along with genome catalogues
+- Application Programming Interface (API)
+
+## Problem in API
+
+- Requires familiarity with API workflows, database structures, and linkages.
+- Leads to challenges in reproducibility and time-consuming data wrangling.
+
+## MGnifyR
+
+- R/Bioconductor package
+- Streamlines access to MGnify database
+- Bridges the gap between data resources and tools
+
+![](images/mgnifyr_logo.png){width="100"}
+
+## Functions
+
+- `MgnifyClient()`: Constructor for `MgnifyClient` object.
+- `doQuery()`: Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.
+- `searchAnalysis()`: Look up analysis accession IDs for one or more study or sample accessions.
+- `getMetadata()`: Get all study, sample and analysis metadata for the supplied analysis accessions.
+- `getResult()`: Get microbial and/or functional profiling data for a list of accessions.
+- `getData()`: Versatile function to retrieve raw results.
+- `getFile()` & `searchFile()`: Download any MGnify files, also including processed reads and identified protein sequences.
+
+## Bioconductor and MGnifyR
+
+- Microbial and functional profiling data is retrieved as [`TreeSE`/`MAE`](https://microbiome.github.io/OMA/docs/devel/pages/containers.html) format.
+- Common data format supported broadly by Bioconductor.
+- Enables direct access to cutting-edge tools (e.g. _miaverse_).
+
+![](images/BioconductorSticker1.png){width="250"}
+![](images/mia_logo.png){width="250"}