CDNMscrna

Materials for single-cell RNA-seq (and other modes of single cell genomics) workshop at Channing

To render the workshop content (first draft)

• install quarto
• use BiocManager::install(c("scRNAseq", "scuttle", "SingleR", "plotly", "ggplot2")) # maybe more?
• use a recent version of Rstudio
• open the .qmd file (after cloning this repo or downloading the qmd) and let Rstudio render it

Some topics that may be addressed in this (or future) workshop(s)

• [available] Basic reference-based cell annotation with SingleR and HumanPrimaryCellAtlas; use the “Get started” tab above
• [available] Introduction to working with cellxgene.census
• [available] Using CuratedAtlasQueryR for filtering the Human Cell Atlas
  • the README at the source is useful
  • a preprint
• [planned] Overview of the OSCA book
• [planned] Overview of the best practices book
• [planned] Exploring catlas.org’s scATACseq collection
• [planned] Overview of the spatial transcriptomics book
• [planned] Using lemur for cluster-free differential expression between experiment groups in single-cell RNA-seq