update tutorial (#3)

.gitignore

@@ -7,4 +7,5 @@ _freeze
 chapters/zilinois_lung_with_celltypist/
 *whee.h5
 *.tiledb
-*_cache
+*_cache
+*_files

_quarto.yml

@@ -1,41 +1,59 @@
 project:
-  type: book
+  type: website
   output-dir: docs
 
 execute:
   freeze: auto
   cache: true
 
-book:
+website:
   title: "Bioc2024: Interoperability between R and Python using BiocPy"
-  author: "[Jayaram Kancherla](mailto:jayaram.kancherla@gmail.com)"
-  contributor: "[Aaron Lun](mailto:infinite.monkeys.with.keys@gmail.com)"
-  favicon: ./assets/short.png
-  site-url: https://biocpy.github.io/tutorial
-  date: "5/31/2024"
-  search: true
-  repo-url: https://github.com/BiocPy/tutorial
-  repo-actions: [issue]
-  # downloads: [pdf, epub]
-  sharing: [twitter]
-  twitter-card: true
-  cover-image: ./assets/full.png
-  page-footer:
-    center: 
-      - text: "(c) BiocPy core contributors"
-        # href: chapters/summary.qmd
   sidebar:
-    style: docked
-    background: light
-  chapters:
-    - index.qmd
-    - tutorials/annotate_cell_types.qmd
-    - tutorials/sessioninfo.qmd
-    # - chapters/references.qmd
+    # search: true
+    contents:
+      - index.qmd
+      - section: "Tutorials"
+        contents:
+          - tutorials/annotate_cell_types.qmd
+          - tutorials/sessioninfo
+
+  # navbar:
+  #   left:
+  #     - href: index.qmd
+  #       text: Home
+  #     - tutorials/annotate_cell_types.qmd
+  #     - tutorials/sessioninfo
+
+# book:
+#   title: "Bioc2024: Interoperability between R and Python using BiocPy"
+#   author: "[Jayaram Kancherla](mailto:jayaram.kancherla@gmail.com)"
+#   contributor: "[Aaron Lun](mailto:infinite.monkeys.with.keys@gmail.com)"
+#   favicon: ./assets/short.png
+#   site-url: https://biocpy.github.io/tutorial
+#   date: "5/31/2024"
+#   search: true
+#   repo-url: https://github.com/BiocPy/tutorial
+#   repo-actions: [issue]
+#   # downloads: [pdf, epub]
+#   sharing: [twitter]
+#   twitter-card: true
+#   cover-image: ./assets/full.png
+#   page-footer:
+#     center: 
+#       - text: "(c) BiocPy core contributors"
+#         # href: chapters/summary.qmd
+#   sidebar:
+#     style: docked
+#     background: light
+#   chapters:
+#     - index.qmd
+#     - tutorials/annotate_cell_types.qmd
+#     - tutorials/sessioninfo.qmd
+#     # - chapters/references.qmd
 
 format:
   html:
-    theme: cosmo
+    theme: sandstone
     number-sections: false
     code-link: true
     toc: true

index.qmd

@@ -1,18 +1,18 @@
 # Welcome
 
-The BiocPy project aims to facilitate development of Bioconductor workflows in Python. 
-
-This tutorial for the workshop will provide an overview of the core data structures implemented in BiocPy 
-(e.g., `GenomicRanges`, `SummarizedExperiment`) that were ported from R. 
-Participants will be guided through two Bioconductor-derived workflows in Python. 
-The first will involve reading an RDS file containing genomic ranges and performing 
-downstream range-based analyses. 
-The second will use the `scRNAseq` package to access public single-cell RNA-seq datasets, 
-followed by cell type annotation using the `SinglePy` package. 
-Attendees will learn how to represent and manipulate their datasets in Python in the 
-same manner as in R/Bioconductor. 
-
-All packages in BiocPy are published to PyPI, and code is open-source on [GitHub](https://github.com/BiocPy).
+Welcome to our workshop on exploring the data structures and packages 
+available in [BiocPy](https://github.com/biocpy), a project that brings 
+the power of Bioconductor to Python. 
+
+In this workshop, we will focus on interoperability between R and Python, covering two main topics:
+
+- Reading an RDS file containing `GenomicRanges` and performing downstream range-based analyses.
+- Annotating single-cell RNA-seq data analysis using the [scrnaseq](https://github.com/biocpy/scrnaseq) package.
+
+Attendees will learn how to represent and manipulate their datasets in Python 
+in the same manner as in R/Bioconductor. 
+All packages in BiocPy are published to PyPI, and the code is open-source 
+on [GitHub](https://github.com/BiocPy).
 
 
 ### Core contributors

requirements.txt

@@ -18,4 +18,6 @@ seaborn
 session-info
 celldex
 scrnaseq
-anndata
+anndata
+matplotlib
+scanpy

rpackages.R

@@ -1,3 +1,3 @@
 install.packages(c("BiocManager"), repos='http://cran.us.r-project.org')
 library(BiocManager)
-BiocManager::install(c("scRNAseq", "celldex", "SingleR", "scuttle", "reticulate", "rmarkdown", "knitr", "downlit", "xml2"))
+BiocManager::install(c("scRNAseq", "celldex", "SingleR", "scuttle", "reticulate", "rmarkdown", "knitr", "downlit", "xml2", "ggplot2", "edgeR"))