HCA session: another shot at getting the image to render

README.md

@@ -1,11 +1,5 @@
 # Orchestrating Single-Cell Analysis with Bioconductor
 
-This is a pre-alpha adaptation of the 2023 ISMB OSCA tutorial using The Carpentries Workbench lesson template. 
-
-### Vignettes converted
-
-As individual vignettes are converted into lessons, they can be added to `config.yaml` to be rendered and shown in the final Github Pages lesson.  
-
 ## Description
 
 In the last few years, the profiling of a large number of genome-wide features
@@ -44,5 +38,8 @@ In particular, participants will learn:
 
 ## Source
 
-This lesson is a template lesson that uses [The Carpentries Workbench](https://carpentries.github.io/sandpaper-docs/) and is based on materials from the [OSCA tutorial at the ISMB 2023](https://bioconductor.github.io/ISMB.OSCA/).
+This lesson uses [The Carpentries Workbench](https://carpentries.github.io/sandpaper-docs/) and is based on materials from the [OSCA tutorial at the ISMB 2023](https://bioconductor.github.io/ISMB.OSCA/).
+
+As individual vignettes are converted into lessons, they can be added to `config.yaml` to be rendered and shown in the final Github Pages lesson.  
+
 

episodes/hca.Rmd

@@ -69,7 +69,9 @@ bulk counts are also available to facilitate large-scale, summary analyses of
 transcriptional profiles. This platform offers a standardized workflow for
 accessing atlas-level datasets programmatically and reproducibly.
 
-![](figures/curatedAtlasQuery.png)
+```{r, echo = FALSE}
+knitr::include_graphics("https://raw.githubusercontent.com/ccb-hms/osca-workbench/main/episodes/figures/curatedAtlasQuery.png")
+```
 
 ## Data Sources in R / Bioconductor
 

episodes/intro-sce.Rmd

@@ -104,7 +104,7 @@ Users should be able to analyze their data using functions from different Biocon
 This class implements a data structure that stores all aspects of our single-cell data - gene-by-cell expression data, per-cell metadata and per-gene annotation - and manipulate them in a synchronized manner.
 
 ```{r, echo=FALSE}
-knitr::include_graphics("http://bioconductor.org/books/3.17/OSCA.intro/images/SingleCellExperiment.png")
+knitr::include_graphics("http://bioconductor.org/books/release/OSCA.intro/images/SingleCellExperiment.png")
 ```
 
 Let's start with an example dataset.