diff --git a/communities/spoc/lab/sections/1_beginner.yml b/communities/spoc/lab/sections/1_beginner.yml index ea4c4fd8..620491a8 100644 --- a/communities/spoc/lab/sections/1_beginner.yml +++ b/communities/spoc/lab/sections/1_beginner.yml @@ -41,13 +41,13 @@ tabs: 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! - EBI SCXA Data Retrieval - 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 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! + # EBI SCXA Data Retrieval + # 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. @@ -60,25 +60,25 @@ tabs: 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. - Scanpy Read10x - 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: Seurat Read10x - 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: DropletUtils Read10x - 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 + #- title_md: Importing 10X Files + # description_md: > + # You can find many tools for importing 10X formatted data into target datatypes. + # Scanpy Read10x + # 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: Seurat Read10x + # 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: DropletUtils Read10x + # 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 - id: data_convert title: Converting datatypes @@ -86,34 +86,34 @@ tabs: 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: SCEasy Converter - 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: SCEasy Converter + # 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: Manipulate AnnData 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: AnnData Operations - 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 +# 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: AnnData Operations +# 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. @@ -121,67 +121,67 @@ tabs: button_icon: tutorial button_tip: View tutorial - - id: data_viz - title: Visualising Data - heading_md: > - There are a few key tools for visualising single-cell data in Galaxy. - content: - - title_md: Plot with Scanpy - 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: Scanpy PlotEmbed - 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: Scanpy PlotTrajectory - 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: Scanpy Plot dimension reduction - 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: Plot with Seurat - 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: data_viz +# title: Visualising Data +# heading_md: > +# There are a few key tools for visualising single-cell data in Galaxy. +# content: +# - title_md: Plot with Scanpy +# 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: Scanpy PlotEmbed +# 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: Scanpy PlotTrajectory + # 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: Scanpy Plot dimension reduction + # 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: Plot with Seurat + # 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