GitHub repository to collect all the materials for a workshop given by Mark D. Robinson at Uni. Freiburg 25.11.2022
- Install R 4.2.x, RStudio (now Posit)
- Install Bioconductor 3.15 (or higher) packages
- Install
quarto - Connect with GitHub ?
# more details at https://bioconductor.org/install/
install.packages("BiocManager")
BiocManager::install(version = "3.15")
pkgs <- c("DropletUtils", "SingleCellExperiment", "SingleR", "batchelor",
"bluster", "dplyr", "edgeR", "ggplot2", "miloR", "muscat",
"patchwork", "pheatmap", "scDblFinder", "scRNAseq", "scater",
"scran", "scuttle","slingshot","tradeSeq")
BiocManager::install(pkgs)
BiocManager::valid()
Download data from here
- TODO: add links here
| Time | Topic | Material |
|---|---|---|
| 09.00-10.20 | preliminaries | session1_preliminaries |
| 10.20-10.40 | coffee break | |
| 10.40-12.00 | QC, normalization, visualization | session2_qc-normalization-viz |
| 12.00-13.00 | lunch break | |
| 13.00-14.20 | differential abundance, differential state | session3_integation-da-ds |
| 14.20-14.40 | coffee break | |
| 14.40-16.00 | trajectories, variations of DA/DS, wrap-up | session4_advanced |
| 16.00 | hard stop | |
| 16.13 | ICE75 @ Freiburg Hbf |
- The morning session was done with live coding; see live_coding_25nov2022
- The afternoon session was done by going through my preparation scripts; see demo_website
- Note to self: send
quartoinstall instructions before hand; a few had issues installing it (e.g., needed new RStudio version) - Some slides used were posted here
- Some notes collected in the YOPAD were cut/paste here