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Add 1st draft for the microgalaxy lab
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| ../../microgalaxy/lab |
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| # If GitHub username, name and avatar will be fetched and displayed | ||
| bebatut | ||
| zierep |
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| # microGalaxy subdomain/Lab | ||
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| # Request this as a webpage with: | ||
| # https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/base.yml | ||
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| # ----------------------------------------------------------------------------- | ||
| # Use these variables in HTML templates like: | ||
| # "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" | ||
| # To make the content more generic and reusable across sites | ||
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| # These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" | ||
| site_name: Australia | ||
| lab_name: microGalaxy Lab | ||
| analysis_name: microGalaxy | ||
| nationality: Australian | ||
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| # Used for rendering tool/workflow links. Trailing '/' will be removed. | ||
| galaxy_base_url: https://singlecell.usegalaxy.org | ||
| subdomain: singlecell | ||
| root_domain: usegalaxy.org | ||
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| # This will enable a feedback form on the webpage: | ||
| # feedback_email: [email protected] | ||
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| support_url: https://help.galaxyproject.org | ||
| # quota_request_url: https://help.galaxyproject.org | ||
| data_policy_url: https://usegalaxy.org/static/terms.html | ||
| terms_url: https://usegalaxy.org/static/terms.html | ||
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| help_links: | ||
| - title: General Galaxy support | ||
| url: https://galaxyproject.org/support/ | ||
| - title: Single Cell help forum | ||
| url: https://help.galaxyproject.org/tag/single-cell | ||
| - title: General Galaxy help forum | ||
| url: https://help.galaxyproject.org | ||
| - title: Galaxy Training Network Slack workspace | ||
| url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg | ||
| - title: Single cell Slack channel (#single-cell-users) | ||
| url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7 | ||
| - title: Single cell user community chat room (Same channel but using Matrix/Element) | ||
| url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im | ||
| - title: Galaxy Training Community chat | ||
| url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im | ||
| - title: Usegalaxy.org chat | ||
| url: https://matrix.to/#/#galaxyproject_Lobby:gitter.im | ||
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| intro_extra_md: "" | ||
| conclusion_extra_md: "" | ||
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| # ----------------------------------------------------------------------------- | ||
| # Custom content relative to this file URL | ||
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| header_logo: static/logo_single_cell.svg | ||
| custom_css: static/custom.css | ||
| intro_md: templates/intro.html | ||
| conclusion_md: templates/conclusion.html | ||
| footer_md: templates/footer.html | ||
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| # Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements. | ||
| # Either: | ||
| # 1. Relative to this file URL | ||
| # 2. Full URL to fetch globally centralized content | ||
| sections: | ||
| - sections/1_beginner.yml | ||
| - sections/3_advanced.yml | ||
| - sections/4_community.yml | ||
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| # ----------------------------------------------------------------------------- |
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| id: beginner | ||
| title: Learn to use Galaxy for microbial data analysis | ||
| tabs: | ||
| - id: learning_pathway | ||
| title: Learning pathways | ||
| heading_md: > | ||
| Connected tutorials to train you to perform single-cell analysis fast! | ||
| content: | ||
| - title_md: Introduction to Galaxy and Sequence analysis | ||
| description_md: > | ||
| This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. | ||
| New to Galaxy and/or the field of genomics? Follow this {gtn modal}[learning path to get familiar with the basics](https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html)! | ||
| button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html | ||
| button_icon: tutorial | ||
| button_tip: Go to learning pathway | ||
| - title_md: Genome annotation for prokaryotes | ||
| description_md: > | ||
| Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. | ||
| Check out the {gtn modal}[Genome annotation for prokaryotes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html). | ||
| button_link: https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html | ||
| button_icon: tutorial | ||
| button_tip: Go to learning pathway | ||
| - title_md: Detection of AMR genes in bacterial genomes | ||
| description_md: > | ||
| This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. | ||
| Check out the {gtn modal}[Detection of AMR genes in bacterial genomes learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). | ||
| button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html | ||
| button_icon: tutorial | ||
| button_tip: Go to learning pathway | ||
| - title_md: Metagenomics data processing and analysis for microbiome | ||
| description_md: > | ||
| This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications | ||
| Check out the {gtn modal}[Metagenomics data processing and analysis for microbiome learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html). | ||
| button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html | ||
| button_tip: Go to learning pathway | ||
| button_icon: tutorial | ||
| - title_md: Clinical metaproteomics workflows within Galaxy | ||
| description_md: > | ||
| This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis. | ||
| Check out the {gtn modal}[Clinical metaproteomics workflows within Galaxy learning pathway](https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html). | ||
| button_link: https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html | ||
| button_tip: View training menu | ||
| button_icon: tutorial | ||
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||
| - id: bacterial_genomics_tutorial | ||
| title: Bacterial genomics tutorials | ||
| heading_md: > | ||
| Using public data is free! Learn how to retrieve data from common sources. | ||
| content: | ||
| - title_md: Importing files from the Single Cell Expression Atlas | ||
| description_md: > | ||
| You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix! | ||
| <code>EBI SCXA Data Retrieval</code> | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: Importing from public atlases - Tutorial | ||
| description_md: > | ||
| You can learn more by following our dedicated to tutorial for importing files from public atlases. | ||
| button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/tutorial.html | ||
| button_icon: tutorial | ||
| button_tip: View tutorial | ||
| - title_md: Importing from NCBI/GEO | ||
| description_md: > | ||
| Where there isn't a specific tool for retrieving data, you can nevertheless import and reformat data from the commonly used NCBI/GEO repository with the following tutorial. | ||
| button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html | ||
| button_icon: tutorial | ||
| button_tip: View tutorial | ||
| - title_md: Importing 10X Files | ||
| description_md: > | ||
| You can find many tools for importing 10X formatted data into target datatypes. | ||
| <code>Scanpy Read10x</code> | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Seurat Read10x</code> | ||
| description_md: > | ||
| Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>DropletUtils Read10x</code> | ||
| description_md: > | ||
| DropletUtils provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
|
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||
| - id: data_convert | ||
| title: Converting datatypes | ||
| heading_md: > | ||
| Single-cell data comes in many formats. | ||
| Here we show a few key tools in Galaxy for converting and manipulating objects in Galaxy. | ||
| content: | ||
| - title_md: <code>SCEasy Converter</code> | ||
| description_md: > | ||
| This tool allows you to convert between the following formats: | ||
| - `hdf5` (AnnData/Loom) | ||
| - `rds` (Seurat) | ||
| - `rdata.sce` (Single Cell Experiment) | ||
| - `h5` (Seurat) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Manipulate AnnData</code> | ||
| description_md: > | ||
| Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as: | ||
| - `Concatenate along the observations axis` for combining AnnData objects together | ||
| - `Transpose the data matrix` for help with converting formats | ||
| - `Filter observations or variables` for refining or subsetting your dataset | ||
| - `Adding annotations` and `Rename categories` for manipulating metadata | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>AnnData Operations</code> | ||
| description_md: > | ||
| This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata. | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: Data conversion training | ||
| description_md: > | ||
| You can also explore our dedicated tutorial on single-cell data conversion. | ||
| button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" | ||
| button_icon: tutorial | ||
| button_tip: View tutorial | ||
|
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||
| - id: data_viz | ||
| title: Visualising Data | ||
| heading_md: > | ||
| There are a few key tools for visualising single-cell data in Galaxy. | ||
| content: | ||
| - title_md: <code>Plot with Scanpy</code> | ||
| description_md: > | ||
| This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. | ||
| inputs: | ||
| - label: Single cell data | ||
| datatypes: | ||
| - hdf5 (AnnData) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Scanpy PlotEmbed</code> | ||
| description_md: > | ||
| This tool allows you to plot embeddings like UMAPs. | ||
| inputs: | ||
| - label: Single cell data | ||
| datatypes: | ||
| - hdf5 (AnnData) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Scanpy PlotTrajectory</code> | ||
| description_md: > | ||
| This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. | ||
| inputs: | ||
| - label: Single cell data | ||
| datatypes: | ||
| - hdf5 (AnnData) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Scanpy Plot dimension reduction</code> | ||
| description_md: > | ||
| This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. | ||
| inputs: | ||
| - label: Single cell data | ||
| datatypes: | ||
| - rds (Seurat object) | ||
| - rdata.sce (Single Cell Experiment) | ||
| - h5 (Seurat) | ||
| - hdf5 (Loom/AnnData) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
| - title_md: <code>Plot with Seurat</code> | ||
| description_md: > | ||
| This tool allows you to plot gene expressions, such as with Violin Plots. | ||
| inputs: | ||
| - label: Single cell data | ||
| datatypes: | ||
| - rds (Seurat object) | ||
| - rdata.sce (Single Cell Experiment) | ||
| - h5 (Seurat) | ||
| - hdf5 (Loom/AnnData) | ||
| button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot" | ||
| button_icon: run | ||
| button_tip: Run tool | ||
|
|
||
| - id: help | ||
| title: Help | ||
| content: | ||
| - title_md: Single Cell help forum | ||
| description_md: > | ||
| Of course! Check out the Galaxy Project | ||
| [Single cell help forum](https://help.galaxyproject.org/tag/scrna) | ||
| - title_md: Troubleshooting errors | ||
| description_md: > | ||
| Find specific advice for | ||
| {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) | ||
| on the GTN. | ||
| - title_md: Can I upload sensitive data? | ||
| description_md: > | ||
| No, please do not upload personal or sensitive, such as human health or clinical data. Please see our | ||
| [Privacy Policy]({{ data_policy_url }}) | ||
| page for definitions of sensitive and health-related information. | ||
| Please also make sure you have read our | ||
| [Terms of Service]({{ terms_url }}), | ||
| which covers hosting and analysis of research data. | ||
| - title_md: Is my data private? | ||
| description_md: > | ||
| Please read our | ||
| [Privacy Policy]({{ data_policy_url }}) | ||
| for information on your personal data and any data that you upload. | ||
| - title_md: How can I increase my storage quota? | ||
| description_md: > | ||
| Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. | ||
| button_md: Request | ||
| button_link: "{{ quota_request_url }}" | ||
| exclude_from: | ||
| - usegalaxy.org | ||
| - title_md: Galaxy {{ site_name }} support | ||
| description_md: > | ||
| Any user of Galaxy {{ site_name }} can request support online! | ||
| button_md: Request support | ||
| button_link: "{{ support_url }}" |
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| id: intermediate | ||
| title: Advanced analysis | ||
| tabs: | ||
| - id: workflows | ||
| title: Multiomic Analyses | ||
| content: | ||
| - title_md: These tutorials use different methods to analyse scRNA-seq samples. | ||
| description_md: > | ||
| {gtn modal}[Learn more](https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/) | ||
| <iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=single-cell" height="600px" width="100%"></iframe> | ||
| - id: deconvolution | ||
| title: Deconvolution | ||
| heading_md: > | ||
| These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference | ||
| These tutorials use different methods to analyse scRNA-seq samples. | ||
| <a href="https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/" target="_blank">Learn more.</a> | ||
| content: [] | ||
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| - id: tips | ||
| title: Tips, tricks & other hints | ||
| heading_md: > | ||
| These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference | ||
| These tutorials use different methods to analyse scRNA-seq samples. | ||
| <a href="https://training.galaxyproject.org/training-material/topics/single-cell/#st-end-to-end/" target="_blank">Learn more.</a> | ||
| content: | ||
| - title_md: About these workflows | ||
| description_md: > | ||
| Hello! Mehmet working here | ||
| button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html#tip-creating-a-new-history | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: Spare space for another GTN | ||
| description_md: > | ||
| More GTN |
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