Single cell RNA-seq Workflow

Highly recommend: Seurat Guided Tutorial

Great bioinformatics tutorial YouTube channel: Collection of Online Tutorials

Folder breakdown

1. analysis contains scripts for Seurat V5 scRNA-seq workflow from loading the files in to annotation, GSEA and optional analysis like trajectory analysis and cell-cell communication.
2. RShiny contains RShiny code that allows the user to interactively view Seurat or CellChat data.
3. scripts contains miscellaneous scripts related to analysis, like Seurat Object to AnnData conversion, or making some plots of interest.

Citations

1. Seurat v5:
   Hao, Y., Stuart, T., Kowalski, M.H. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 42, 293–304 (2024). https://doi.org/10.1038/s41587-023-01767-y
2. Harmony:
   Korsunsky, I., Millard, N., Fan, J. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16, 1289–1296 (2019). https://doi.org/10.1038/s41592-019-0619-0
3. clusterProfiler:
   Yu G (2024). “Thirteen years of clusterProfiler.” The Innovation, 5(6), 100722. doi:10.1016/j.xinn.2024.100722, https://doi.org/10.1016/j.xinn.2024.100722.
4. fgsea:
   Korotkevich G, Sukhov V, Sergushichev A (2019). “Fast gene set enrichment analysis.” bioRxiv. doi:10.1101/060012, http://biorxiv.org/content/early/2016/06/20/060012.
5. CellChat:
   Jin, S., Guerrero-Juarez, C.F., Zhang, L. et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 12, 1088 (2021). https://doi.org/10.1038/s41467-021-21246-9
6. Liana:
   Dimitrov, D., Schäfer, P.S.L., Farr, E. et al. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol 26, 1613–1622 (2024). https://doi.org/10.1038/s41556-024-01469-w
7. ShinyCell:
   John F Ouyang, Uma S Kamaraj, Elaine Y Cao, Owen J L Rackham, ShinyCell: simple and sharable visualization of single-cell gene expression data, Bioinformatics, Volume 37, Issue 19, October 2021, Pages 3374–3376, https://doi.org/10.1093/bioinformatics/btab209
8. CellChat Shiny:
   https://github.com/sqjin/CellChatShiny