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
- [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