Home - MattHuff/scRNASeq_011224 GitHub Wiki

Welcome to the scRNASeq_011224 wiki! This wiki serves as a documentation of another single-cell RNASeq (scRNASeq) dataset. Though it is largely similar to the initial pipeline, it has key differences due to not using 10X reads.

1. Quality Control - FastQC
2. Trimming Reads - Skewer
3. Align and Quantify Counts - Cell Ranger
4. Remove Ambient RNA - Cellbender
5. Data Clustering - Seurat
6. Remove Doublets - ScDblFinder
7. Find Markers - Presto
8. Celltype Annotation - Manual Annotation
9. Differential Gene Expression - MAST
10. GO Analysis - EnrichR
11. Pathway Analysis - MSigDBR