dependencies

Author: stemangiola

.gitignore

@@ -7,6 +7,6 @@ TidyGenomicsTranscriptomicsWorkshop_bioc2023.Rproj
 .DS_Store
 /doc/
 /Meta/
-vignettes/tidySpatialWorkshop225_cache/
-vignettes/tidySpatialWorkshop225_files/
-tidySpatialWorkshop225.Rproj
+vignettes/tidySpatialWorkshop2025_cache/
+vignettes/tidySpatialWorkshop2025_files/
+tidySpatialWorkshop2025.Rproj

DESCRIPTION

@@ -1,6 +1,6 @@
-Package: tidySpatialWorkshop225
+Package: tidySpatialWorkshop2025
 Title: Workshop Materials for Tidy Spatial Analysis
-Version: 0.18.1
+Version: 0.18.2
 Authors@R: c(
     person("Stefano", "Mangiola", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7474-836X")),
@@ -61,7 +61,8 @@ Suggests:
     here,
     igraph,
     magick,
-    scatterpie
+    scatterpie,
+    ggcorrplot
 VignetteBuilder: knitr
-URL: https://github.com/tidyomics/tidySpatialWorkshop225
-BugReports: https://github.com/tidyomics/tidySpatialWorkshop225/issues
+URL: https://github.com/tidyomics/tidySpatialWorkshop2025
+BugReports: https://github.com/tidyomics/tidySpatialWorkshop2025/issues

R/data_transcriptomics.R

@@ -92,7 +92,7 @@
 #'
 #' @format A gate object compatible with tidygate and tidySpatialExperiment::gate()
 #'
-#' @source Created during the Tidy Spatial Workshop 225 using interactive gating
+#' @source Created during the Tidy Spatial Workshop 2025 using interactive gating
 #'   on Visium spatial transcriptomics data from the spatialLIBD package
 #'
 #' @examples

README.md

@@ -1,8 +1,8 @@
-# tidySpatialWorkshop225
+# tidySpatialWorkshop2025
 
 <!-- badges: start -->
 [![DOI](https://zenodo.org/badge/379767139.svg)](https://zenodo.org/badge/latestdoi/379767139)
-[![Check, build, and push image](https://github.com/tidyomics/tidySpatialWorkshop225/actions/workflows/basic_checks.yaml/badge.svg)](https://github.com/tidyomics/tidySpatialWorkshop225/actions/workflows/basic_checks.yaml)
+[![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)
 <!-- badges: end -->
 
 ## Instructor names and contact information
@@ -12,7 +12,7 @@
 
 ## Syllabus
 
-Material [web page](https://tidyomics.github.io/tidySpatialWorkshop225/)
+Material [web page](https://tidyomics.github.io/tidySpatialWorkshop2025/)
 
 More details on the workshop are below.
 
@@ -33,9 +33,9 @@ Bioconductor 3.19.
 
 # Install workshop package
 #install.packages('BiocManager')
-BiocManager::install("tidyomics/tidySpatialWorkshop225", dependencies = TRUE)
+BiocManager::install("tidyomics/tidySpatialWorkshop2025", dependencies = TRUE)
 
-# In May 225, 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
+# 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", 
@@ -47,28 +47,28 @@ BiocManager::install(c("lmweber/ggspavis",
 BiocManager::install("ggcorrplot")
     
 # Then build the vignettes
-BiocManager::install("tidyomics/tidySpatialWorkshop225", build_vignettes = TRUE, force=TRUE)
+BiocManager::install("tidyomics/tidySpatialWorkshop2025", build_vignettes = TRUE, force=TRUE)
 
 # To view vignette
-library(tidySpatialWorkshop225)
+library(tidySpatialWorkshop2025)
 vignette("Introduction")
 ```
 
 ## Interactive execution of the vignettes
 
-From command line, and enter the tidySpatialWorkshop225 directory.
+From command line, and enter the tidySpatialWorkshop2025 directory.
 
 ```
 # Open the command line
-git clone [email protected]:tidyomics/tidySpatialWorkshop225.git
+git clone [email protected]:tidyomics/tidySpatialWorkshop2025.git
 
 ```
 
-Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop225/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
+Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop2025/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/tidySpatialWorkshop225/blob/devel/vignettes/Session_1_sequencing_assays.Rmd)
+[R markdown file](https://github.com/tidyomics/tidySpatialWorkshop2025/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/tidySpatialWorkshop225
+url: https://tidyomics.github.io/tidySpatialWorkshop2025
 
 template:
   params:
     bootswatch: flatly
     #ganalytics: UA-99999999-9
 
 home:
-  title: "tidySpatialWorkshop225"
+  title: "tidySpatialWorkshop2025"
   type: inverse
 
 navbar:
   right:
    - icon: fa-github
-     href: https://github.com/tidyomics/tidySpatialWorkshop225
+     href: https://github.com/tidyomics/tidySpatialWorkshop2025

inst/vignettes/tidyomics.bib

@@ -87,7 +87,7 @@ @Article{ Lee2020
 VOLUME = {9},
 YEAR = {2020},
 NUMBER = {109},
-DOI = {10.12688/f1000research.22259.1}
+DOI = {10.12688/f1000research.220259.1}
 }
 
 @article{Love2020,

man/spatial_data_gated.Rd

@@ -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='tidySpatialWorkshop225', 'bibliography'), 'bibliography.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', '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/tidySpatialWorkshop225/articles/main.html).
+[here](https://tidyomics.github.io/tidySpatialWorkshop2025/articles/main.html).
 
 ## Workshop package installation 
 
@@ -66,38 +66,27 @@ Bioconductor 3.19.
 
 # Install workshop package
 #install.packages('BiocManager')
-BiocManager::install("tidyomics/tidySpatialWorkshop225", dependencies = TRUE)
-
-# In May 225, 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/tidySpatialWorkshop225", build_vignettes = TRUE, force=TRUE)
+BiocManager::install("tidyomics/tidySpatialWorkshop", build_vignettes = TRUE, force=TRUE)
 
 # To view vignette
-library(tidySpatialWorkshop225)
+library(tidySpatialWorkshop2025)
 vignette("Introduction")
 ```
 
 ## Interactive execution of the vignettes
 
-From command line, and enter the tidySpatialWorkshop225 directory.
+From command line, and enter the tidySpatialWorkshop2025 directory.
 
 ```
 # Open the command line
-git clone [email protected]:tidyomics/tidySpatialWorkshop225.git
+git clone [email protected]:tidyomics/tidySpatialWorkshop2025.git
 
 ```
 
-Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop225/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
+Alternatively download the [git zipped package](https://github.com/tidyomics/tidySpatialWorkshop2025/archive/refs/heads/devel.zip). Uncompress it. And enter the directory. 
 
 # Announcements
 

vignettes/Introduction.Rmd

@@ -3,7 +3,7 @@ title: "Sequencing assays"
 author:
   - Stefano Mangiola, South Australian immunoGENomics Cancer Institute^[<[email protected]>], Walter and Eliza Hall Institute^[<mangiola.s at wehi.edu.au>]
 output: rmarkdown::html_vignette
-# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop225', 'vignettes'), 'tidyomics.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', 'vignettes'), 'tidyomics.bib')`"
 vignette: >
   %\VignetteIndexEntry{Sequencing assays}
   %\VignetteEncoding{UTF-8}
@@ -569,7 +569,7 @@ Overview of the algorithm
 
 - \* Combine these three matrices by direct product
 
-[Singhal et al., 225](https://www.nature.com/articles/s41588-024-01664-3)
+[Singhal et al., 2025](https://www.nature.com/articles/s41588-024-01664-3)
 
 [Material source](https://bioconductor.org/packages/release/bioc/vignettes/Banksy/inst/doc/multi-sample.html)
 
@@ -764,7 +764,7 @@ SPOTlight uses a seeded non-negative matrix factorization regression, initialize
 
 Harmonised data is stored in the ARDC Nectar Research Cloud, and most cellNexus functions interact with Nectar via web requests, so a network connection is required for most functionality.
 
-Mangiola et al., 225 doi [doi.org/10.1101/2023.06.08.542671](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
+Mangiola et al., 2025 doi [doi.org/10.1101/2023.06.08.542671](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 
 ```{r, echo=FALSE, out.width="700px"}
 knitr::include_graphics(here("inst/images/curated_atlas_query.png"))

vignettes/Session_1_sequencing_assays.Rmd

@@ -3,7 +3,7 @@ title: "Tidy spatial analyses"
 author:
   - Stefano Mangiola, South Australian immunoGENomics Cancer Institute^[<[email protected]>], Walter and Eliza Hall Institute^[<mangiola.s at wehi.edu.au>]
 output: rmarkdown::html_vignette
-# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop225', 'vignettes'), 'tidyomics.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', 'vignettes'), 'tidyomics.bib')`"
 vignette: >
   %\VignetteIndexEntry{Tidy spatial analyses}
   %\VignetteEncoding{UTF-8}
@@ -24,12 +24,12 @@ library(here)
 
 A good introduction of `tidyomics` can be found here
 
-[tidySpatialWorkshop225](https://github.com/tidyomics/tidySpatialWorkshop225) 
+[tidySpatialWorkshop2025](https://github.com/tidyomics/tidySpatialWorkshop2025) 
 [tidy transcriptomic manifesto](https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/)
 
 `tidyomics` is an interoperable software ecosystem that bridges Bioconductor and the tidyverse. `tidyomics` is installable with a single homonymous meta-package. This ecosystem includes three new packages: tidySummarizedExperiment, tidySingleCellExperiment, and tidySpatialExperiment, and five publicly available R packages: `plyranges`, `nullranges`, `tidyseurat`, `tidybulk`, `tidytof`. Importantly, `tidyomics` leaves the original data containers and methods unaltered, ensuring compatibility with existing software, maintainability and long-term Bioconductor support. 
 
-`tidyomics` is presented in "The tidyomics ecosystem: Enhancing omic data analyses" [Hutchison and Keyes et al., 225](https://www.biorxiv.org/content/10.1101/2023.09.10.557072v1)
+`tidyomics` is presented in "The tidyomics ecosystem: Enhancing omic data analyses" [Hutchison and Keyes et al., 2025](https://www.biorxiv.org/content/10.1101/2023.09.10.557072v1)
 
 ```{r, echo=FALSE, out.width="700px"}
 knitr::include_graphics(here("inst/images/tidyomics.png"))
@@ -50,7 +50,7 @@ let's make sure we get the latest packages available on github
 
 ```{r, eval=FALSE}
 
-# In May 225, 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
+# 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", 
                         "stemangiola/tidySingleCellExperiment", 
@@ -114,7 +114,7 @@ rownames(spatialCoords(spatial_data)) = colnames(spatial_data) # Bug?
 spatial_data
 ```
 ::: {.note}
-If `ExperimentHub` should not work. The `spatial_data` object from the previous code block can be downloaded from [Zenodo - 10.5281/zenodo.11233385](https://zenodo.org/records/11233385/files/tidySpatialWorkshop225_spatial_data.rds?download=1)
+If `ExperimentHub` should not work. The `spatial_data` object from the previous code block can be downloaded from [Zenodo - 10.5281/zenodo.11233385](https://zenodo.org/records/11233385/files/tidySpatialWorkshop2025_spatial_data.rds?download=1)
 :::
 
 ### 1. tidySpatialExperiment package
@@ -359,7 +359,7 @@ spatial_data =
   filter(in_tissue, sample_id=="151673") |> 
   
   # Gate based on tissue morphology
-  tidySpatialExperiment::gate(alpha = 0.1, colour = "spatialLIBD", programmatic_gates = tidySpatialWorkshop225::spatial_data_gated) 
+  tidySpatialExperiment::gate(alpha = 0.1, colour = "spatialLIBD", programmatic_gates = tidySpatialWorkshop2025::spatial_data_gated) 
 
 ```
 

vignettes/Session_2_Tidy_spatial_analyses.Rmd

@@ -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='tidySpatialWorkshop225', 'vignettes'), 'tidyomics.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', 'vignettes'), 'tidyomics.bib')`"
 vignette: >
   %\VignetteIndexEntry{Imaging assays (tidy)}
   %\VignetteEncoding{UTF-8}
@@ -73,7 +73,7 @@ library(scico)
 
 #### SubcellularSpatialData
 
-This [data package](https://bioconductor.org/packages/release/data/experiment/html/SubcellularSpatialData.html) contains annotated datasets localized at the sub-cellular level from the STOmics, Xenium, and CosMx platforms, as analyzed in the publication by [Bhuva et al., 225](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03241-7). It includes raw transcript detections and provides functions to convert these into `SpatialExperiment` objects.
+This [data package](https://bioconductor.org/packages/release/data/experiment/html/SubcellularSpatialData.html) contains annotated datasets localized at the sub-cellular level from the STOmics, Xenium, and CosMx platforms, as analyzed in the publication by [Bhuva et al., 2025](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03241-7). It includes raw transcript detections and provides functions to convert these into `SpatialExperiment` objects.
 
 ```{r, eval=FALSE}
 
@@ -552,7 +552,7 @@ tx_spe_sample_1 |>
 
 ### 4. Neighborhood analyses
 
-hoodscanR [Liu et al., 225](https://www.bioconductor.org/packages/release/bioc/vignettes/hoodscanR/inst/doc/Quick_start.html)
+hoodscanR [Liu et al., 2025](https://www.bioconductor.org/packages/release/bioc/vignettes/hoodscanR/inst/doc/Quick_start.html)
 
 [Source](https://divingintogeneticsandgenomics.com/post/neighborhood-cellular-niches-analysis-with-spatial-transcriptome-data-in-seurat-and-bioconductor/)
 

vignettes/Session_3_imaging_assays.Rmd

@@ -3,7 +3,7 @@ title: "Sequencing assays"
 author:
   - Stefano Mangiola, South Australian immunoGENomics Cancer Institute^[<[email protected]>], Walter and Eliza Hall Institute^[<mangiola.s at wehi.edu.au>]
 output: rmarkdown::html_vignette
-# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop225', 'vignettes'), 'tidyomics.bib')`"
+# bibliography: "`r file.path(system.file(package='tidySpatialWorkshop2025', 'vignettes'), 'tidyomics.bib')`"
 vignette: >
   %\VignetteIndexEntry{Sequencing assays}
   %\VignetteEncoding{UTF-8}