scRNASeq

single-cell RNA sequencing

This work is licensed under a Creative Commons Attribution 4.0 International License.

Most of the materials from this practical come from the following sources:

• The Orchestrating Single-Cell Analysis with Bioconductor book
• The Spatter vignettes
• The Seurat vignettes
• The Kallisto-Bustools tutorials
• The Bioconductor vignettes of the R packages used
• The monocle vignette
• The TradSeq vignette

Please run the following command before the practical:

In a bash shell:

singularity run /data/share/MADT/TP_lmodolo/lbmc-tp_scrna\:0.2.0.sif
# singularity run docker://lbmc/docker://lbmc/tp_scrna:0.2.0

All the materials are available here: https://gitbio.ens-lyon.fr/LBMC/hub/formations/scrna

Summary

• Introduction
• Nature of the data
• RNA Quantification
• SingleCellExperiment
• Quality Control
• Normalization
• Data analysis
• Trajectory analysis