Merge pull request #4 from tidyomics/improve_vignettes

Improve vignettes

Author: stemangiola

.gitignore

@@ -7,6 +7,6 @@ TidyGenomicsTranscriptomicsWorkshop_bioc2023.Rproj
 .DS_Store
 /doc/
 /Meta/
-vignettes/tidySpatialWorkshop2025_cache/
-vignettes/tidySpatialWorkshop2025_files/
-tidySpatialWorkshop2025.Rproj
+vignettes/tidySpatialWorkshop_cache/
+vignettes/tidySpatialWorkshop_files/
+tidySpatialWorkshop.Rproj

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: tidySpatialWorkshop2025
+Package: tidySpatialWorkshop
 Title: Workshop Materials for Tidy Spatial Analysis
 Version: 0.18.5
 Authors@R: c(
@@ -65,5 +65,5 @@ Suggests:
     scatterpie,
     ggcorrplot
 VignetteBuilder: knitr
-URL: https://github.com/tidyomics/tidySpatialWorkshop2025
-BugReports: https://github.com/tidyomics/tidySpatialWorkshop2025/issues
+URL: https://github.com/tidyomics/tidySpatialWorkshop
+BugReports: https://github.com/tidyomics/tidySpatialWorkshop/issues

README.md

@@ -1,8 +1,8 @@
-# tidySpatialWorkshop2025
+# tidySpatialWorkshop
 
 <!-- badges: start -->
 [![DOI](https://zenodo.org/badge/379767139.svg)](https://zenodo.org/badge/latestdoi/379767139)
-[![Check, build, and push image](https://github.com/tidyomics/tidySpatialWorkshop2025/actions/workflows/basic_checks.yaml/badge.svg)](https://github.com/tidyomics/tidySpatialWorkshop2025/actions/workflows/basic_checks.yaml)
+[![Check, build, and push image](https://github.com/tidyomics/tidySpatialWorkshop/actions/workflows/basic_checks.yaml/badge.svg)](https://github.com/tidyomics/tidySpatialWorkshop/actions/workflows/basic_checks.yaml)
 <!-- badges: end -->
 
 ## Instructor names and contact information
@@ -12,7 +12,7 @@
 
 ## Syllabus
 
-Material [web page](https://tidyomics.github.io/tidySpatialWorkshop2025/)
+Material [web page](https://tidyomics.github.io/tidySpatialWorkshop/)
 
 More details on the workshop are below.
 
@@ -33,42 +33,31 @@ Bioconductor 3.19.
 
 # Install workshop package
 #install.packages('BiocManager')
-BiocManager::install("tidyomics/tidySpatialWorkshop2025", dependencies = TRUE)
-
-# In May 2025, the following packages should be installed from github repositories, to use the latest features. In case you have them pre installed, run the following command
-BiocManager::install(c("lmweber/ggspavis", 
-                       "stemangiola/tidySummarizedExperiment", 
-                       "william-hutchison/tidySpatialExperiment", 
-                       "stemangiola/tidybulk", 
-                       "stemangiola/tidygate", 
-                       "stemangiola/CuratedAtlasQueryR"), 
-                     update = FALSE)
-                     
-BiocManager::install("ggcorrplot")
-    
+BiocManager::install("tidyomics/tidySpatialWorkshop", dependencies = TRUE)
+
 # Then build the vignettes
-BiocManager::install("tidyomics/tidySpatialWorkshop2025", build_vignettes = TRUE, force=TRUE)
+BiocManager::install("tidyomics/tidySpatialWorkshop", build_vignettes = TRUE, force=TRUE)
 
 # To view vignette
-library(tidySpatialWorkshop2025)
-vignette("Introduction")
+library(tidySpatialWorkshop)
+vignette("Session_1_sequencing_assays")
 ```
 
 ## Interactive execution of the vignettes
 
-From command line, and enter the tidySpatialWorkshop2025 directory.
+From command line, and enter the tidySpatialWorkshop directory.
 
 ```
 # Open the command line
-git clone [email protected]:tidyomics/tidySpatialWorkshop2025.git
+git clone [email protected]:tidyomics/tidySpatialWorkshop.git
 
 ```
 
-Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop2025/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
+Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
 
 
 To run the code, you could then copy and paste the code from the workshop vignette or 
-[R markdown file](https://github.com/tidyomics/tidySpatialWorkshop2025/blob/devel/vignettes/Session_1_sequencing_assays.Rmd)
+[R markdown file](https://github.com/tidyomics/tidySpatialWorkshop/blob/devel/vignettes/Session_1_sequencing_assays.Rmd)
 into a new R Markdown file on your computer. 
 
 ## Workshop Description

_pkgdown.yml

@@ -1,15 +1,15 @@
-url: https://tidyomics.github.io/tidySpatialWorkshop2025
+url: https://tidyomics.github.io/tidySpatialWorkshop
 
 template:
   params:
     bootswatch: flatly
     #ganalytics: UA-99999999-9
 
 home:
-  title: "tidySpatialWorkshop2025"
+  title: "tidySpatialWorkshop"
   type: inverse
 
 navbar:
   right:
    - icon: fa-github
-     href: https://github.com/tidyomics/tidySpatialWorkshop2025
+     href: https://github.com/tidyomics/tidySpatialWorkshop

inst/images/stomics.png

@@ -4,7 +4,7 @@ author:
   - Stefano Mangiola, South Australian immunoGENomics Cancer Institute^[<[email protected]>], Walter and Eliza Hall Institute^[<mangiola.s at wehi.edu.au>]
   - Luciano Martellotto, Adelaide Centre for Epigenetics, South Australian immunoGENomics Cancer Institute^[<[email protected]>]
 output: rmarkdown::html_vignette
-# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', 'bibliography'), 'bibliography.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop', 'bibliography'), 'bibliography.bib')`"
 vignette: >
   %\VignetteIndexEntry{Introduction to Spatial omic analyses}
   %\VignetteEncoding{UTF-8}
@@ -54,7 +54,7 @@ knitr::include_graphics(here("inst/images/physalia-min.png"))
 
 You can view the material at the workshop webpage
 
-[here](https://tidyomics.github.io/tidySpatialWorkshop2025/articles/main.html).
+[here](https://tidyomics.github.io/tidySpatialWorkshop/index.html).
 
 ## Workshop package installation 
 
@@ -72,24 +72,25 @@ BiocManager::install("tidyomics/tidySpatialWorkshop", dependencies = TRUE)
 BiocManager::install("tidyomics/tidySpatialWorkshop", build_vignettes = TRUE, force=TRUE)
 
 # To view vignette
-library(tidySpatialWorkshop2025)
+library(tidySpatialWorkshop)
 vignette("Introduction")
 ```
 
 ## Interactive execution of the vignettes
 
-From command line, and enter the tidySpatialWorkshop2025 directory.
+From command line, and enter the tidySpatialWorkshop directory.
 
 ```
 # Open the command line
-git clone [email protected]:tidyomics/tidySpatialWorkshop2025.git
+git clone [email protected]:tidyomics/tidySpatialWorkshop.git
 
 ```
 
-Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop2025/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
+Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
 
 # Announcements
 
+Tidyomics is now published in (Nature Methods)[https://www.nature.com/articles/s41592-024-02299-2]. And availabel for (free) here[https://www.biorxiv.org/content/10.1101/2023.09.10.557072v3].
 
 # Introduction to Spatial Omics
 
@@ -100,35 +101,65 @@ sequencing in experimental and analytical contexts.
 
 ### Workshop Structure
 
-#### 1. Welcome and Introduction
+#### Day 1
 
--   Overview of the workshop.
--   Goals for Day 1.
+##### 1. Welcome and Introduction
 
-#### 2. What is Spatial Omics?
+-   Introduction of the instructor
+-   Introduction of the crowd
+-   Overview and goals of the workshop.
+
+##### 2. What is Spatial Omics?
 
 -   Definition and significance in modern biology.
 -   Key applications and impact.
-
-#### 3. Technologies in Spatial Omics
-
 -   Overview of different spatial omics technologies.
 -   Comparison of imaging-based vs sequencing-based approaches.
 
-#### 4. Sequencing Spatial Omics
+##### 3. Sequencing Spatial Omics
 
 -   Detailed comparison of methodologies.
 -   Experimental design considerations.
 -   Data analysis challenges and solutions.
 
-#### 5. Overview of Analysis Frameworks
+##### 5. Analysis of sequencing based spatial data
+
+-   Getting Started with SpatialExperiment.
+-   Data Visualisation and Manipulation.
+-   Quality control and filtering.
+-   Dimensionality reduction.
+-   Spatial Clustering.
+-   Deconvolution of pixel-based spatial data.
+
+#### Day 2
+
+##### 1. Introduction to tidyomics
+
+-   Use tidyverse on spatial, single-cell, pseudobulk and bulk genomic data   
 
--   Introduction to various analysis frameworks.
--   Brief mention of 'tidy' data principles in spatial omics.
+##### 2. Working with tidySpatialExperiment
+
+-   tidySpatialExperiment package
+-   Tidyverse commands
+-   Advanced filtering/gating and pseudobulk
+-   Work with features
+-   Summarisation/aggregation
+-   tidyfying your workflow
+-   Visualisation
+
+#### Day 3
+
+##### 1. Imaging Spatial Omics
+
+-   Detailed comparison of methodologies.
+-   Experimental design considerations.
+-   Data analysis challenges and solutions.
 
-#### 6. Wrap-Up and Q&A
+##### 2. Spatial analyses of imaging data
 
--   Summarize key takeaways.
--   Open floor for questions and discussions.
+-   Working with imaging-based data in Bioconductor with MoleculeExperiment
+-   Aggregation and analysis
+-   Clustering
+-   Neighborhood analyses