scRNA-seq Trajectory Inference
Parameters
Count table file: Select “waterson_counts.tsv“
Experimental Design File: Select “waterson_cell_metadata.tsv“
Normalization Method: Log Normalization
PCA-Dimensions: 50
PCA-Scaling: Checked
Add Gene Subset File: Unchecked
Add optional Gene Information: Checked
Gene Information: Select “waterson_gene_annotations.tsv“
Remove batch effects: Checked
Batch-Column with batch information: Choose “batch“
Mutual Nearest Neighbor: 20
UMAP-Min. Distance: 0.1
UMAP- Neighbours: 15
Clustering-Nearest Neighbor: 20
Disjoint Graphs: Unchecked
Loops: Unchecked
Select Starting Point: Choose Experimental Design File
Select Column: Choose “raw.embryo.time.bin“
Starting Point: Choose “170-210“