diff --git a/episodes/hca.Rmd b/episodes/hca.Rmd index 211cb6d..5f7fcef 100644 --- a/episodes/hca.Rmd +++ b/episodes/hca.Rmd @@ -6,13 +6,15 @@ exercises: 10 # Minutes of exercises in the lesson :::::::::::::::::::::::::::::::::::::: questions -- TODO +- How to obtain comprehensive single-cell reference maps from the Human Cell Atlas? :::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::: objectives -- TODO +- Learn about different resources for public single-cell RNA-seq data. +- Learn how to access data from the Human Cell Atlas using the CuratedAtlasQueryR package. +- Learn how to query for cells of interest and how to download them into a SingleCellExperiment object. :::::::::::::::::::::::::::::::::::::::::::::::: @@ -67,11 +69,7 @@ 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. -```{r,echo=FALSE} -knitr::include_graphics( - "figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" -) -``` +![](figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png) # Data Sources in R / Bioconductor @@ -85,16 +83,16 @@ There are a few options to access single cell data with R / Bioconductor. # Installation -```{r,eval=FALSE} +```{r, eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") -BiocManager::install("stemangiola/CuratedAtlasQueryR") +BiocManager::install("CuratedAtlasQueryR") ``` # Package load -```{r,include=TRUE,results="hide",message=FALSE,warning=FALSE} +```{r, include = TRUE, results = "hide", message = FALSE, warning = FALSE} library(CuratedAtlasQueryR) library(dplyr) ``` @@ -105,7 +103,7 @@ The metadata allows the user to get a lay of the land of what is available via the package. In this example, we are using the sample database URL which allows us to get a small and quick subset of the available metadata. -```{r} +```{r, message = FALSE} metadata <- get_metadata(remote_url = CuratedAtlasQueryR::SAMPLE_DATABASE_URL) ``` @@ -151,7 +149,7 @@ metadata |> # Columns available in the metadata -```{r} +```{r, message = FALSE} head(names(metadata), 10) ``` @@ -180,7 +178,7 @@ data. ### Query raw counts -```{r} +```{r, message = FALSE} single_cell_counts <- metadata |> dplyr::filter( @@ -199,7 +197,7 @@ single_cell_counts This is helpful if just few genes are of interest, as they can be compared across samples. -```{r} +```{r, message = FALSE} metadata |> dplyr::filter( ethnicity == "African" & @@ -212,7 +210,7 @@ metadata |> ### Extract only a subset of genes -```{r} +```{r, message = FALSE} single_cell_counts <- metadata |> dplyr::filter( @@ -334,7 +332,7 @@ possible. :::::::::::::: solution -```{r} +```{r, message = FALSE} metadata |> dplyr::filter( sex == "female" & @@ -356,11 +354,3 @@ metadata |> :::::::::::::::::::::::::::::::::::::::::::::::: -# Acknowledgements - -Thank you to [Stefano Mangiola](https://github.com/stemangiola) and his team for -developing -[CuratedAtlasQueryR](https://github.com/stemangiola/CuratedAtlasQueryR) and -graciously providing the content from their vignette. Make sure to keep an eye -out for their publication for proper citation. Their bioRxiv paper can be found -at .