Package index • leo.sc

Basic Functions

Core workflow functions located in R/basic.R

read_sc_data(): Read single-cell data into a Seurat object
seurat_standard_normalize_and_scale(): Standard seurat normalize_and_scale
seurat_basic_qc(): Seurat basic QC
plot_qc(): Plot QC metrics
doublet_removal(): Remove doublets using DoubletFinder
doublet_rate_dictionary(): Lookup expected doublet rate based on cells loaded
seurat_basic_info(): get basic summary of a seurat object
remove_unwant_hvg(): Remove unwanted HVGs
subset_srt(): Subset srt obj easily
write_10x_triple(): Export Seurat object to 10x-style triple files
metadata_write_10x(): Export Seurat meta.data aligned to barcodes

Metadata manipulation functions located in R/metadata.R

metadata_get_colnames(): Get specified metadata columns from a Seurat object
metadata_keep(): Keep only selected metadata columns in a Seurat object
metadata_drop(): Drop specified metadata columns from a Seurat object

Marker identification and annotation utilities located in R/annotation.R

format_markers_for_upload(): Format marker-gene lists for (bulk) upload
sort_string_numeric_clusters(): Sort string-based cluster labels numerically and refactor
get_cluster_counts(): Get cluster counts sorted descending
filter_clusters_by_percent_or_cell_count(): Filter Seurat clusters by percentage or absolute cell count
calcROGUE(): Calculate and plot ROGUE index for a Seurat object, with inline filtering
score_signature(): Score sc_obj with signature list
plot_score_signature_heatmap(): Plot heatmap of signature scores
locate_most_different_g_in_2_group(): Locate most distinguishing markers between two clusters
gimme_marker(): Give me marker!

Built-in markers and reference data located in R/dict.R

Advanced cell type analysis located in R/celltype.R

Virtual gene perturbation simulations located in R/sko.R

Functions for handling multi-batch datasets located in R/multi_batch.R

check_gene_stats_in_multi_batch() check_gene_avg_in_multi_batch() subset_common_gene_in_multi_batch(): Inspection of gene in multi-batch

Generic plotting utilities located in R/sc.plot.R