diff --git a/episodes/intro_bioc_sce.Rmd b/episodes/intro_bioc_sce.Rmd index e482f46..0e72bdc 100644 --- a/episodes/intro_bioc_sce.Rmd +++ b/episodes/intro_bioc_sce.Rmd @@ -1,14 +1,22 @@ --- title: Introduction to Bioconductor and the SingleCellExperiment class -vignette: > - % \VignetteIndexEntry{Introduction} - % \VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} -output: - html_document: - mathjax: null +teaching: 10 # Minutes of teaching in the lesson +exercises: 2 # Minutes of exercises in the lesson --- +:::::::::::::::::::::::::::::::::::::: questions + +- What is Bioconductor? +- How is single-cell data store in the Bioconductor ecosystem? + +:::::::::::::::::::::::::::::::::::::::::::::::: + +::::::::::::::::::::::::::::::::::::: objectives + +- TODO + +:::::::::::::::::::::::::::::::::::::::::::::::: + # Setup ```{r setup, message = FALSE, warning=FALSE} @@ -92,24 +100,50 @@ library(scater) plotReducedDim(sce, "pca.corrected.E8.5", colour_by = "celltype.mapped") ``` +:::::::::::::::::::::::::::::::::: challenge -# Session Info +#### Exercise 1 -```{r sessionInfo} -sessionInfo() -``` +Create a `SingleCellExperiment` object: Try and create a SingleCellExperiment object "from scratch". Start from a matrix (either randomly generated or with some fake data in it) and add one or more columns as colData. -# Further Reading +:::::::::::::: hint -* OSCA book, [Introduction](https://bioconductor.org/books/release/OSCA.intro) +The `SingleCellExperiment` function can be used to create a new SingleCellExperiment object + +::::::::::::::::::::::: + +:::::::::::::: solution + +TODO +::::::::::::::::::::::: + +::::::::::::::::::::::::::::::::::::::::::::: -# Exercises +:::::::::::::::::::::::::::::::::: challenge -1. Create a `SingleCellExperiment` object: Try and create a SingleCellExperiment object "from scratch". Start from a matrix (either randomly generated or with some fake data in it) and add one or more columns as colData. +#### Exercise 2 + +Combining two objects: The `MouseGastrulationData` package contains several datasets. Download sample 6 of the chimera experiment by running `sce6 <- WTChimeraData(sample=6)`. Use the `cbind` function to combine the new data with the `sce` object created before. + +:::::::::::::: solution + +TODO +::::::::::::::::::::::: + +::::::::::::::::::::::::::::::::::::::::::::: + + +::::::::::::::::::::::::::::::::::::: keypoints + +- TODO + +:::::::::::::::::::::::::::::::::::::::::::::::: + +# Further Reading + +* OSCA book, [Introduction](https://bioconductor.org/books/release/OSCA.intro) -Hint: the `SingleCellExperiment` function can be used to create a new SingleCellExperiment object. -2. Combining two objects: The `MouseGastrulationData` package contains several datasets. Download sample 6 of the chimera experiment by running `sce6 <- WTChimeraData(sample=6)`. Use the `cbind` function to combine the new data with the `sce` object created before. diff --git a/episodes/cell_type_annotation.Rmd b/old-lessons/cell_type_annotation.Rmd similarity index 100% rename from episodes/cell_type_annotation.Rmd rename to old-lessons/cell_type_annotation.Rmd diff --git a/episodes/eda_qc.Rmd b/old-lessons/eda_qc.Rmd similarity index 100% rename from episodes/eda_qc.Rmd rename to old-lessons/eda_qc.Rmd diff --git a/old-lessons/figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png b/old-lessons/figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png new file mode 100644 index 0000000..4f32b9e Binary files /dev/null and b/old-lessons/figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png differ diff --git a/episodes/hca.Rmd b/old-lessons/hca.Rmd similarity index 100% rename from episodes/hca.Rmd rename to old-lessons/hca.Rmd diff --git a/episodes/large_data.Rmd b/old-lessons/large_data.Rmd similarity index 100% rename from episodes/large_data.Rmd rename to old-lessons/large_data.Rmd diff --git a/episodes/multi_sample.Rmd b/old-lessons/multi_sample.Rmd similarity index 100% rename from episodes/multi_sample.Rmd rename to old-lessons/multi_sample.Rmd