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All functions

SeuratPipe
SeuratPipe: Streamlining Seurat analysis
add_umap_embedding()
Add UMAP embedding in Seurat object
cluster_analysis()
Common clustering analysis steps
compute_module_score()
Tailored module score calculation
create_seurat_object()
Create Seurat object based on sample metadata.
dim_plot()
Tailored dimensional reduction plot
dim_plot_tailored()
Tailored dim plot
dimred_qc_plots()
QC and general metadata plots visualised on dimensional reduced space
dot_plot()
Tailored dot plot
feature_plot()
Tailored feature plot
feature_plot_tailored()
Tailored feature plot
find_all_markers()
Wrapper FindAllMarkers function
find_clusters()
Wrapper FindClusters function
find_neighbors()
Tailored function for finding neighbors in lower dimensional space.
harmony_analysis()
Analysis steps for Harmony integration
heatmap_plot()
Tailored heatmap plot
install_scrublet()
Install Scrublet Python Package
lognormalize_and_pca()
Log normalisation and PCA computation
module_score_analysis()
Module score analysis
pca_feature_cor_plot()
PCA and feature metadata correlation heatmap plot
qc_filter_seurat_object()
Filter Seurat object based on QC metrics.
run_cluster_pipeline()
Pipeline for clustering analysis
run_harmony()
Local implementation of RunHarmony function
run_harmony_pipeline()
Pipeline for Harmony integration
run_qc_pipeline()
QC pipeline
run_spatial_qc_pipeline()
Spatial QC pipeline
run_umap()
Tailored UMAP function
scatter_meta_plot()
Tailored scatter plot of metadata
spatial_create_seurat_object()
Create Seurat object based on spatial sample metadata.
spatial_dim_plot()
Tailored spatial dim plot
spatial_feature_plot()
Tailored spatial feature plot
subset_dim_plot()
Subset dim plot
subset_feature_plot()
Subset feature plot