Scripts for analyzing single cell RNAseq data
| File Name | Description |
|---|---|
| scRNAseq_standard_workflow.Rmd | Basic scRNAseq workflow (QC, dimensionality reduction, clustering, annotation) |
| NMF_scRNAseq.Rmd | Non-negative matrix factorization to ID expression modules |
| blastema_analysis.Rmd | Analysis of a cell-type specific cluster over time |
| scTE.Rmd | Analysis of transposable element expression |
| CellPhoneDB.Rmd | Analysis of ligand/receptor relationships between cell types |
| MAGIC.Rmd | Using MAGIC to impute and smooth scRNAseq data, and explore cell state transitions |